rs7547615

Variant names:

• chr1-193106964-T-C
• rs7547615

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 0.61 in 151,918 control chromosomes in the GnomAD database, including 28,963 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 0.61 (28963 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.296
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.747 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: 0.610 AC: 92567 AN: 151800 Hom.: 28946 Cov.: 32

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.666

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.767

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.674

Gnomad OTH AF: 0.643

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

GnomAD4 genome AF: 0.610 AC: 92625 AN: 151918 Hom.: 28963 Cov.: 32 AF XY: 0.612 AC XY: 45433 AN XY: 74234

African (AFR) AF: 0.474 AC: 19632 AN: 41412

American (AMR) AF: 0.666 AC: 10174 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.678 AC: 2352 AN: 3470

East Asian (EAS) AF: 0.452 AC: 2336 AN: 5172

South Asian (SAS) AF: 0.767 AC: 3687 AN: 4804

European-Finnish (FIN) AF: 0.611 AC: 6411 AN: 10494

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.674 AC: 45797 AN: 67976

Other (OTH) AF: 0.645 AC: 1360 AN: 2108

Alfa AF: 0.618 Hom.: 4518

Bravo AF: 0.602

Asia WGS AF: 0.640 AC: 2218 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	6.2
DANN	Benign	0.88
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs7547615; hg19: chr1-193076094;