7-86634364-T-G

Position:

• chr7-86634364-T-G

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 0.306 in 152,088 control chromosomes in the GnomAD database, including 8,774 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 0.31 (8774 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.341

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.698 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: 0.306 AC: 46558 AN: 151968 Hom.: 8758 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.718

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.328

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.306 AC: 46592 AN: 152088 Hom.: 8774 Cov.: 32 AF XY: 0.317 AC XY: 23560 AN XY: 74318

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.473

Gnomad4 ASJ AF: 0.312

Gnomad4 EAS AF: 0.717

Gnomad4 SAS AF: 0.592

Gnomad4 FIN AF: 0.328

Gnomad4 NFE AF: 0.322

Gnomad4 OTH AF: 0.331

Alfa AF: 0.282 Hom.: 1242

Bravo AF: 0.309

Asia WGS AF: 0.564 AC: 1959 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.5
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs187993; hg19: chr7-86263680;