rs1503813

Variant names:

• chr1-161730889-A-G
• rs1503813
• ENST00000826671.1:n.144-317T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-161730889-A-G
• chr1-161730889-A-T

Variant summary

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

The ENST00000826671.1(ENSG00000307516):​n.144-317T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 152,046 control chromosomes in the GnomAD database, including 3,678 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 0.21 (3678 hom., cov: 31)
• Consequence: ENSG00000307516 ENST00000826671.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.311
• Publications: 9 publications found

Genes affected

ENSG00000307516 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307516	ENST00000826671.1	n.144-317T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31417 AN: 151928 Hom.: 3666 Cov.: 31

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.236

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.207 AC: 31441 AN: 152046 Hom.: 3678 Cov.: 31 AF XY: 0.209 AC XY: 15552 AN XY: 74324

African (AFR) AF: 0.119 AC: 4954 AN: 41480

American (AMR) AF: 0.359 AC: 5490 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 981 AN: 3470

East Asian (EAS) AF: 0.218 AC: 1125 AN: 5162

South Asian (SAS) AF: 0.174 AC: 839 AN: 4820

European-Finnish (FIN) AF: 0.226 AC: 2389 AN: 10556

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.221 AC: 15005 AN: 67970

Other (OTH) AF: 0.236 AC: 499 AN: 2110

Alfa AF: 0.221 Hom.: 5033

Bravo AF: 0.218

Asia WGS AF: 0.263 AC: 916 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	6.3
DANN	Benign	0.84
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs1503813; hg19: chr1-161700679;