rs77689838

Variant names:

• chr7-68126052-C-T
• rs77689838

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 0.0953 in 152,128 control chromosomes in the GnomAD database, including 1,097 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 0.095 (1097 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.162
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.209 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: 0.0952 AC: 14471 AN: 152010 Hom.: 1094 Cov.: 33

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.0498

Gnomad ASJ AF: 0.0331

Gnomad EAS AF: 0.0760

Gnomad SAS AF: 0.0986

Gnomad FIN AF: 0.0547

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0447

Gnomad OTH AF: 0.0833

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

GnomAD4 genome AF: 0.0953 AC: 14493 AN: 152128 Hom.: 1097 Cov.: 33 AF XY: 0.0959 AC XY: 7128 AN XY: 74352

African (AFR) AF: 0.213 AC: 8837 AN: 41466

American (AMR) AF: 0.0498 AC: 761 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0331 AC: 115 AN: 3472

East Asian (EAS) AF: 0.0757 AC: 391 AN: 5162

South Asian (SAS) AF: 0.0985 AC: 475 AN: 4824

European-Finnish (FIN) AF: 0.0547 AC: 579 AN: 10594

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0447 AC: 3043 AN: 68006

Other (OTH) AF: 0.0839 AC: 177 AN: 2110

Alfa AF: 0.0831 Hom.: 284

Bravo AF: 0.0998

Asia WGS AF: 0.0970 AC: 337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.4
DANN	Benign	0.68
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs77689838; hg19: chr7-67591039;