chr7-136461788-C-A

Variant names:

• chr7-136461788-C-A
• rs10250997

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 0.143 in 152,010 control chromosomes in the GnomAD database, including 1,963 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 0.14 (1963 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.531
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.244 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: 0.143 AC: 21744 AN: 151892 Hom.: 1962 Cov.: 32

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.0812

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.0137

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.143 AC: 21750 AN: 152010 Hom.: 1963 Cov.: 32 AF XY: 0.141 AC XY: 10479 AN XY: 74308

African (AFR) AF: 0.248 AC: 10260 AN: 41444

American (AMR) AF: 0.0811 AC: 1238 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 416 AN: 3472

East Asian (EAS) AF: 0.0138 AC: 71 AN: 5154

South Asian (SAS) AF: 0.131 AC: 632 AN: 4816

European-Finnish (FIN) AF: 0.113 AC: 1198 AN: 10588

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7538 AN: 67948

Other (OTH) AF: 0.122 AC: 258 AN: 2112

Alfa AF: 0.121 Hom.: 3781

Bravo AF: 0.145

Asia WGS AF: 0.0840 AC: 291 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	1.7
DANN	Benign	0.54
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs10250997; hg19: chr7-136146536;