7-86634364-T-G

Variant names:

• chr7-86634364-T-G
• rs187993

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 0.306 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
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.698 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: 0.306 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

African (AFR) AF: 0.128 AC: 5312 AN: 41518

American (AMR) AF: 0.473 AC: 7231 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.312 AC: 1082 AN: 3470

East Asian (EAS) AF: 0.717 AC: 3693 AN: 5148

South Asian (SAS) AF: 0.592 AC: 2853 AN: 4816

European-Finnish (FIN) AF: 0.328 AC: 3465 AN: 10558

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.322 AC: 21913 AN: 67974

Other (OTH) AF: 0.331 AC: 700 AN: 2116

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.5
DANN	Benign	0.35
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs187993; hg19: chr7-86263680;