chr7-54114239-C-T

Variant names:

• chr7-54114239-C-T
• rs6593122

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 0.188 in 152,146 control chromosomes in the GnomAD database, including 2,759 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 0.19 (2759 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.847
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.198 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: 0.188 AC: 28565 AN: 152028 Hom.: 2754 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.0501

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.188 AC: 28597 AN: 152146 Hom.: 2759 Cov.: 32 AF XY: 0.191 AC XY: 14206 AN XY: 74364

African (AFR) AF: 0.178 AC: 7386 AN: 41512

American (AMR) AF: 0.204 AC: 3112 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 559 AN: 3470

East Asian (EAS) AF: 0.0501 AC: 259 AN: 5174

South Asian (SAS) AF: 0.160 AC: 771 AN: 4826

European-Finnish (FIN) AF: 0.223 AC: 2354 AN: 10560

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.199 AC: 13560 AN: 68010

Other (OTH) AF: 0.154 AC: 324 AN: 2106

Alfa AF: 0.188 Hom.: 5993

Bravo AF: 0.187

Asia WGS AF: 0.139 AC: 486 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.71
DANN	Benign	0.66
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs6593122; hg19: chr7-54181932;