7-38096675-T-C

Position:

• chr7-38096675-T-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.600

Gnomad4 AMR AF: 0.473

Gnomad4 ASJ AF: 0.567

Gnomad4 EAS AF: 0.571

Gnomad4 SAS AF: 0.494

Gnomad4 FIN AF: 0.701

Gnomad4 NFE AF: 0.583

Gnomad4 OTH AF: 0.574

Alfa AF: 0.582 Hom.: 30861

Bravo AF: 0.570

Asia WGS AF: 0.551 AC: 1912 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1524058; hg19: chr7-38136277;