rs2001740

Variant names:

• chr10-50027147-T-C
• rs2001740
• ENST00000457608.1:n.217A>G

Variant summary

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

The ENST00000457608.1(SLC9A3P3):​n.217A>G variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.147 in 166,752 control chromosomes in the GnomAD database, including 2,627 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 0.13 (1747 hom., cov: 33)
  • Exomes 𝑓: 0.31 (880 hom.)
• Consequence: SLC9A3P3 ENST00000457608.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.95
• Publications: 1 publications found

Genes affected

SLC9A3P3 (HGNC:33492): (solute carrier family 9 member 3 pseudogene 3)

FAM21EP (HGNC:):

FAM21EP (HGNC:45010): (family with sequence similarity 21 member E, pseudogene)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC9A3P3		n.50027147T>C		intragenic_variant
FAM21EP	NR_038275.2	n.1892-5680A>G		intron_variant	Intron 6 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC9A3P3	ENST00000457608.1	n.217A>G		non_coding_transcript_exon_variant	Exon 1 of 1	6
FAM21EP	ENST00000456967.5	n.1892-5680A>G		intron_variant	Intron 6 of 6	2
FAM21EP	ENST00000649244.2	n.1161-5680A>G		intron_variant	Intron 9 of 9

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19964 AN: 152078 Hom.: 1745 Cov.: 33

Gnomad AFR AF: 0.0745

Gnomad AMI AF: 0.0736

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.0780

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.147

GnomAD4 exome AF: 0.315 AC: 4580 AN: 14556 Hom.: 880 Cov.: 0 AF XY: 0.317 AC XY: 2944 AN XY: 9290

African (AFR) AF: 0.169 AC: 30 AN: 178

American (AMR) AF: 0.691 AC: 600 AN: 868

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 98 AN: 244

East Asian (EAS) AF: 0.590 AC: 248 AN: 420

South Asian (SAS) AF: 0.306 AC: 1132 AN: 3698

European-Finnish (FIN) AF: 0.196 AC: 260 AN: 1324

Middle Eastern (MID) AF: 0.263 AC: 140 AN: 532

European-Non Finnish (NFE) AF: 0.283 AC: 1890 AN: 6690

Other (OTH) AF: 0.302 AC: 182 AN: 602

GnomAD4 genome AF: 0.131 AC: 19983 AN: 152196 Hom.: 1747 Cov.: 33 AF XY: 0.131 AC XY: 9750 AN XY: 74406

African (AFR) AF: 0.0743 AC: 3088 AN: 41538

American (AMR) AF: 0.259 AC: 3961 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 597 AN: 3472

East Asian (EAS) AF: 0.276 AC: 1429 AN: 5172

South Asian (SAS) AF: 0.168 AC: 809 AN: 4818

European-Finnish (FIN) AF: 0.0780 AC: 827 AN: 10606

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.130 AC: 8856 AN: 67988

Other (OTH) AF: 0.149 AC: 314 AN: 2110

Alfa AF: 0.129 Hom.: 201

Bravo AF: 0.146

Asia WGS AF: 0.238 AC: 831 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	12
DANN	Benign	0.55
PhyloP100		3.9

Splicing

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

Other links and lift over

dbSNP: rs2001740; hg19: chr10-51786907;