rs7547615

chr1-193106964-T-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.474

Gnomad4 AMR AF: 0.666

Gnomad4 ASJ AF: 0.678

Gnomad4 EAS AF: 0.452

Gnomad4 SAS AF: 0.767

Gnomad4 FIN AF: 0.611

Gnomad4 NFE AF: 0.674

Gnomad4 OTH AF: 0.645

Alfa AF: 0.623 Hom.: 4436

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7547615; hg19: chr1-193076094;