rs1547958

Variant names:

• chr7-150943197-C-T
• rs1547958

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 0.164 in 152,248 control chromosomes in the GnomAD database, including 2,688 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 0.16 (2688 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.642
• Publications: 9 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 (NFE) allele frequency at 95% confidence interval = 0.238 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: 0.164 AC: 24899 AN: 152130 Hom.: 2684 Cov.: 33

Gnomad AFR AF: 0.0419

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.0474

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.164 AC: 24894 AN: 152248 Hom.: 2688 Cov.: 33 AF XY: 0.160 AC XY: 11920 AN XY: 74444

African (AFR) AF: 0.0418 AC: 1736 AN: 41566

American (AMR) AF: 0.164 AC: 2514 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 658 AN: 3468

East Asian (EAS) AF: 0.0475 AC: 246 AN: 5174

South Asian (SAS) AF: 0.205 AC: 991 AN: 4830

European-Finnish (FIN) AF: 0.159 AC: 1683 AN: 10612

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.241 AC: 16387 AN: 67982

Other (OTH) AF: 0.181 AC: 382 AN: 2110

Alfa AF: 0.214 Hom.: 11947

Bravo AF: 0.156

Asia WGS AF: 0.138 AC: 478 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	1.8
DANN	Benign	0.49
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs1547958; hg19: chr7-150640285;