7-38096675-T-C

Variant names:

• chr7-38096675-T-C
• rs1524058

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 0.581 in 152,014 control chromosomes in the GnomAD database, including 25,928 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 0.58 (25928 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.17
• Publications: 28 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 = 0.593 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: 0.580 AC: 88156 AN: 151896 Hom.: 25889 Cov.: 32

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.570

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.701

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.570

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

GnomAD4 genome AF: 0.581 AC: 88263 AN: 152014 Hom.: 25928 Cov.: 32 AF XY: 0.580 AC XY: 43115 AN XY: 74282

African (AFR) AF: 0.600 AC: 24860 AN: 41460

American (AMR) AF: 0.473 AC: 7224 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.567 AC: 1964 AN: 3464

East Asian (EAS) AF: 0.571 AC: 2945 AN: 5162

South Asian (SAS) AF: 0.494 AC: 2381 AN: 4820

European-Finnish (FIN) AF: 0.701 AC: 7395 AN: 10556

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.583 AC: 39598 AN: 67962

Other (OTH) AF: 0.574 AC: 1214 AN: 2114

Alfa AF: 0.583 Hom.: 79336

Bravo AF: 0.570

Asia WGS AF: 0.551 AC: 1912 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.19
DANN	Benign	0.44
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs1524058; hg19: chr7-38136277;