7-122993600-C-T

Variant names:

• chr7-122993600-C-T
• rs6466849

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 0.195 in 151,904 control chromosomes in the GnomAD database, including 2,977 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 0.20 (2977 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.181
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.26 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: 0.195 AC: 29621 AN: 151786 Hom.: 2983 Cov.: 32

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.195 AC: 29624 AN: 151904 Hom.: 2977 Cov.: 32 AF XY: 0.192 AC XY: 14234 AN XY: 74252

African (AFR) AF: 0.218 AC: 9016 AN: 41424

American (AMR) AF: 0.174 AC: 2652 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 703 AN: 3470

East Asian (EAS) AF: 0.197 AC: 1012 AN: 5130

South Asian (SAS) AF: 0.272 AC: 1309 AN: 4814

European-Finnish (FIN) AF: 0.144 AC: 1521 AN: 10544

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.187 AC: 12734 AN: 67968

Other (OTH) AF: 0.178 AC: 374 AN: 2106

Alfa AF: 0.115 Hom.: 210

Bravo AF: 0.198

Asia WGS AF: 0.233 AC: 810 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.0
DANN	Benign	0.65
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs6466849; hg19: chr7-122633654;