7-10849858-G-A

Variant names:

• chr7-10849858-G-A
• rs968794

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 0.377 in 142,588 control chromosomes in the GnomAD database, including 10,314 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 0.38 (10314 hom., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.377 AC: 53784 AN: 142544 Hom.: 10316 Cov.: 24

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.335

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.377 AC: 53787 AN: 142588 Hom.: 10314 Cov.: 24 AF XY: 0.380 AC XY: 26233 AN XY: 68950

African (AFR) AF: 0.277 AC: 10582 AN: 38162

American (AMR) AF: 0.379 AC: 5386 AN: 14206

Ashkenazi Jewish (ASJ) AF: 0.514 AC: 1751 AN: 3404

East Asian (EAS) AF: 0.336 AC: 1646 AN: 4894

South Asian (SAS) AF: 0.477 AC: 2169 AN: 4550

European-Finnish (FIN) AF: 0.427 AC: 3469 AN: 8126

Middle Eastern (MID) AF: 0.420 AC: 110 AN: 262

European-Non Finnish (NFE) AF: 0.414 AC: 27362 AN: 66108

Other (OTH) AF: 0.423 AC: 838 AN: 1982

Alfa AF: 0.386 Hom.: 17371

Bravo AF: 0.361

Asia WGS AF: 0.387 AC: 1328 AN: 3442

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.50
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs968794; hg19: chr7-10889485;