chr7-123208562-C-T

Variant names:

• chr7-123208562-C-T
• rs10487974

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 0.335 in 151,436 control chromosomes in the GnomAD database, including 9,168 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 0.33 (9168 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.460
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50667 AN: 151318 Hom.: 9164 Cov.: 31

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.335 AC: 50669 AN: 151436 Hom.: 9168 Cov.: 31 AF XY: 0.340 AC XY: 25182 AN XY: 73992

African (AFR) AF: 0.184 AC: 7626 AN: 41376

American (AMR) AF: 0.387 AC: 5888 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 1516 AN: 3456

East Asian (EAS) AF: 0.371 AC: 1893 AN: 5098

South Asian (SAS) AF: 0.399 AC: 1921 AN: 4810

European-Finnish (FIN) AF: 0.447 AC: 4718 AN: 10546

Middle Eastern (MID) AF: 0.373 AC: 109 AN: 292

European-Non Finnish (NFE) AF: 0.384 AC: 25952 AN: 67654

Other (OTH) AF: 0.324 AC: 680 AN: 2100

Alfa AF: 0.259 Hom.: 729

Bravo AF: 0.323

Asia WGS AF: 0.340 AC: 1181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.4
DANN	Benign	0.71
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs10487974; hg19: chr7-122848616;