ENST00000634870.1:n.3881G>A

Variant names:

• chr1-94615889-C-T
• rs4474258
• ENST00000634870.1:n.3881G>A

Variant summary

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

The ENST00000634870.1(SLC44A3-AS1):​n.3881G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.376 in 152,036 control chromosomes in the GnomAD database, including 10,805 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 0.38 (10804 hom., cov: 32)
  • Exomes 𝑓: 0.50 (1 hom.)
• Consequence: SLC44A3-AS1 ENST00000634870.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.96

Genes affected

SLC44A3-AS1 (HGNC:49057): (SLC44A3 antisense RNA 1)

LOC105378861 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.489 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378861	XR_001738160.3	n.512-19902C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC44A3-AS1	ENST00000634870.1	n.3881G>A		non_coding_transcript_exon_variant	Exon 6 of 6	5

Frequencies

GnomAD3 genomes AF: 0.376 AC: 57167 AN: 151912 Hom.: 10805 Cov.: 32

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.371

GnomAD4 exome AF: 0.500 AC: 2 AN: 4 Hom.: 1 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 2 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.376 AC: 57192 AN: 152032 Hom.: 10804 Cov.: 32 AF XY: 0.380 AC XY: 28225 AN XY: 74306

African (AFR) AF: 0.353 AC: 14644 AN: 41450

American (AMR) AF: 0.384 AC: 5868 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.391 AC: 1358 AN: 3470

East Asian (EAS) AF: 0.505 AC: 2612 AN: 5172

South Asian (SAS) AF: 0.382 AC: 1839 AN: 4820

European-Finnish (FIN) AF: 0.378 AC: 3989 AN: 10544

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.378 AC: 25667 AN: 67984

Other (OTH) AF: 0.370 AC: 779 AN: 2108

Alfa AF: 0.392 Hom.: 14554

Bravo AF: 0.374

Asia WGS AF: 0.429 AC: 1492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4474258; hg19: chr1-95081445;