rs846672

Variant names:

• chr7-122990126-A-C
• rs846672

Your query was ambiguous. Multiple possible variants found:

• chr7-122990126-A-C
• chr7-122990126-A-T

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 0.727 in 152,046 control chromosomes in the GnomAD database, including 41,008 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 0.73 (41008 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.862 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: 0.727 AC: 110465 AN: 151928 Hom.: 40968 Cov.: 33

Gnomad AFR AF: 0.870

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.731

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.671

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.674

Gnomad OTH AF: 0.718

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

GnomAD4 genome AF: 0.727 AC: 110556 AN: 152046 Hom.: 41008 Cov.: 33 AF XY: 0.724 AC XY: 53811 AN XY: 74296

African (AFR) AF: 0.869 AC: 36078 AN: 41508

American (AMR) AF: 0.731 AC: 11162 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.678 AC: 2351 AN: 3470

East Asian (EAS) AF: 0.530 AC: 2730 AN: 5150

South Asian (SAS) AF: 0.672 AC: 3239 AN: 4822

European-Finnish (FIN) AF: 0.656 AC: 6935 AN: 10566

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.674 AC: 45784 AN: 67946

Other (OTH) AF: 0.723 AC: 1526 AN: 2112

Alfa AF: 0.686 Hom.: 25085

Bravo AF: 0.741

Asia WGS AF: 0.670 AC: 2315 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.24
DANN	Benign	0.44
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs846672; hg19: chr7-122630180;