rs787480

Variant names:

• chr1-67630189-G-A
• rs787480

Your query was ambiguous. Multiple possible variants found:

• chr1-67630189-G-A
• chr1-67630189-G-T

Variant summary

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

The variant allele was found at a frequency of 0.307 in 151,938 control chromosomes in the GnomAD database, including 9,016 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 0.31 (9016 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.54 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

Frequencies

GnomAD3 genomes AF: 0.307 AC: 46624 AN: 151820 Hom.: 8995 Cov.: 32

Gnomad AFR AF: 0.546

Gnomad AMI AF: 0.0989

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.307 AC: 46706 AN: 151938 Hom.: 9016 Cov.: 32 AF XY: 0.308 AC XY: 22898 AN XY: 74270

African (AFR) AF: 0.546 AC: 22601 AN: 41394

American (AMR) AF: 0.278 AC: 4248 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 590 AN: 3470

East Asian (EAS) AF: 0.442 AC: 2282 AN: 5166

South Asian (SAS) AF: 0.246 AC: 1184 AN: 4816

European-Finnish (FIN) AF: 0.205 AC: 2156 AN: 10536

Middle Eastern (MID) AF: 0.291 AC: 85 AN: 292

European-Non Finnish (NFE) AF: 0.189 AC: 12847 AN: 67956

Other (OTH) AF: 0.295 AC: 623 AN: 2110

Alfa AF: 0.228 Hom.: 6092

Bravo AF: 0.321

Asia WGS AF: 0.379 AC: 1316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.17
DANN	Benign	0.34
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs787480; hg19: chr1-68095872;