7-85369937-T-C

Variant names:

• chr7-85369937-T-C
• rs10499885

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 0.117 in 152,184 control chromosomes in the GnomAD database, including 1,923 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 0.12 (1923 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.284
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.276 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: 0.117 AC: 17732 AN: 152066 Hom.: 1911 Cov.: 32

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.0539

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.0676

Gnomad FIN AF: 0.0384

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0329

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.117 AC: 17772 AN: 152184 Hom.: 1923 Cov.: 32 AF XY: 0.116 AC XY: 8614 AN XY: 74420

African (AFR) AF: 0.280 AC: 11633 AN: 41484

American (AMR) AF: 0.127 AC: 1934 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0539 AC: 187 AN: 3468

East Asian (EAS) AF: 0.139 AC: 720 AN: 5162

South Asian (SAS) AF: 0.0669 AC: 323 AN: 4830

European-Finnish (FIN) AF: 0.0384 AC: 408 AN: 10614

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0329 AC: 2238 AN: 68028

Other (OTH) AF: 0.109 AC: 230 AN: 2114

Alfa AF: 0.0886 Hom.: 188

Bravo AF: 0.133

Asia WGS AF: 0.141 AC: 492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.1
DANN	Benign	0.79
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs10499885; hg19: chr7-84999253;