rs6974500

Positions:

• chr7-23704930-C-A
• chr7-23704930-C-G

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 0.574 in 151,902 control chromosomes in the GnomAD database, including 26,149 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 0.57 (26149 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.477

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.676 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: 0.574 AC: 87173 AN: 151784 Hom.: 26164 Cov.: 31

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.642

Gnomad SAS AF: 0.697

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.643

Gnomad OTH AF: 0.581

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

GnomAD4 genome AF: 0.574 AC: 87173 AN: 151902 Hom.: 26149 Cov.: 31 AF XY: 0.577 AC XY: 42871 AN XY: 74242

Gnomad4 AFR AF: 0.382

Gnomad4 AMR AF: 0.642

Gnomad4 ASJ AF: 0.624

Gnomad4 EAS AF: 0.641

Gnomad4 SAS AF: 0.696

Gnomad4 FIN AF: 0.660

Gnomad4 NFE AF: 0.643

Gnomad4 OTH AF: 0.576

Alfa AF: 0.634 Hom.: 43859

Bravo AF: 0.560

Asia WGS AF: 0.651 AC: 2261 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.8
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6974500; hg19: chr7-23744549;