7-78008062-G-C

Variant names:

• chr7-78008062-G-C
• rs4729938

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 0.619 in 152,112 control chromosomes in the GnomAD database, including 29,345 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 0.62 (29345 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.48
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.741 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.619 AC: 94141 AN: 151994 Hom.: 29334 Cov.: 33

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.675

Gnomad EAS AF: 0.761

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.621

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.607

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

GnomAD4 genome AF: 0.619 AC: 94198 AN: 152112 Hom.: 29345 Cov.: 33 AF XY: 0.624 AC XY: 46375 AN XY: 74358

African (AFR) AF: 0.618 AC: 25640 AN: 41492

American (AMR) AF: 0.628 AC: 9593 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.675 AC: 2342 AN: 3470

East Asian (EAS) AF: 0.760 AC: 3928 AN: 5166

South Asian (SAS) AF: 0.650 AC: 3137 AN: 4826

European-Finnish (FIN) AF: 0.636 AC: 6725 AN: 10574

Middle Eastern (MID) AF: 0.620 AC: 181 AN: 292

European-Non Finnish (NFE) AF: 0.599 AC: 40747 AN: 67986

Other (OTH) AF: 0.607 AC: 1284 AN: 2114

Alfa AF: 0.532 Hom.: 1628

Bravo AF: 0.620

Asia WGS AF: 0.702 AC: 2440 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.16
DANN	Benign	0.43
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs4729938; hg19: chr7-77637379;