rs3732062

Variant names:

• chr2-65001102-T-C
• rs3732062
• NM_003038.5:c.528-346T>C

Your query was ambiguous. Multiple possible variants found:

• chr2-65001102-T-C
• chr2-65001102-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003038.5(SLC1A4):​c.528-346T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 204,414 control chromosomes in the GnomAD database, including 5,519 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.22 (4380 hom., cov: 32)
  • Exomes 𝑓: 0.18 (1139 hom.)
• Consequence: SLC1A4 NM_003038.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.639
• Publications: 8 publications found

Genes affected

SLC1A4 (HGNC:10942): (solute carrier family 1 member 4) The protein encoded by this gene is a sodium-dependent neutral amino acid transporter for alanine, serine, cysteine, and threonine. Defects in this gene have been associated with developmental delay, microcephaly, and intellectual disability. [provided by RefSeq, Jan 2017]

LINC02245 (HGNC:53134): (long intergenic non-protein coding RNA 2245)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC1A4	NM_003038.5	c.528-346T>C		intron_variant	Intron 1 of 7	ENST00000234256.4	NP_003029.2
SLC1A4	NM_001348406.2	c.-133-346T>C		intron_variant	Intron 1 of 7		NP_001335335.1
SLC1A4	NM_001348407.2	c.-133-346T>C		intron_variant	Intron 1 of 7		NP_001335336.1
SLC1A4	NM_001193493.2	c.-133-346T>C		intron_variant	Intron 1 of 6		NP_001180422.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC1A4	ENST00000234256.4	c.528-346T>C		intron_variant	Intron 1 of 7	1	NM_003038.5	ENSP00000234256.3

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33245 AN: 152018 Hom.: 4376 Cov.: 32

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.553

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.229

GnomAD4 exome AF: 0.178 AC: 9313 AN: 52278 Hom.: 1139 Cov.: 0 AF XY: 0.177 AC XY: 4727 AN XY: 26736

African (AFR) AF: 0.263 AC: 440 AN: 1674

American (AMR) AF: 0.339 AC: 609 AN: 1798

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 264 AN: 1882

East Asian (EAS) AF: 0.530 AC: 1327 AN: 2506

South Asian (SAS) AF: 0.159 AC: 577 AN: 3628

European-Finnish (FIN) AF: 0.178 AC: 473 AN: 2658

Middle Eastern (MID) AF: 0.213 AC: 57 AN: 268

European-Non Finnish (NFE) AF: 0.143 AC: 4902 AN: 34334

Other (OTH) AF: 0.188 AC: 664 AN: 3530

GnomAD4 genome AF: 0.219 AC: 33263 AN: 152136 Hom.: 4380 Cov.: 32 AF XY: 0.223 AC XY: 16616 AN XY: 74388

African (AFR) AF: 0.282 AC: 11705 AN: 41470

American (AMR) AF: 0.301 AC: 4598 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 495 AN: 3470

East Asian (EAS) AF: 0.553 AC: 2855 AN: 5166

South Asian (SAS) AF: 0.187 AC: 901 AN: 4826

European-Finnish (FIN) AF: 0.189 AC: 2000 AN: 10588

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.148 AC: 10066 AN: 68002

Other (OTH) AF: 0.228 AC: 482 AN: 2110

Alfa AF: 0.190 Hom.: 1835

Bravo AF: 0.237

Asia WGS AF: 0.350 AC: 1215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.61
PhyloP100		-0.64
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3732062; hg19: chr2-65228236;