rs6881634

Variant names:

• chr5-78335030-G-A
• rs6881634

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 0.478 in 152,120 control chromosomes in the GnomAD database, including 19,489 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 0.48 (19489 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.612 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: 0.479 AC: 72770 AN: 152002 Hom.: 19492 Cov.: 32

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.0966

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.600

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.502

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

GnomAD4 genome AF: 0.478 AC: 72783 AN: 152120 Hom.: 19489 Cov.: 32 AF XY: 0.473 AC XY: 35181 AN XY: 74372

African (AFR) AF: 0.292 AC: 12100 AN: 41504

American (AMR) AF: 0.422 AC: 6439 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.550 AC: 1909 AN: 3470

East Asian (EAS) AF: 0.0967 AC: 501 AN: 5182

South Asian (SAS) AF: 0.404 AC: 1950 AN: 4826

European-Finnish (FIN) AF: 0.600 AC: 6353 AN: 10580

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.617 AC: 41943 AN: 67974

Other (OTH) AF: 0.500 AC: 1058 AN: 2114

Alfa AF: 0.561 Hom.: 116769

Bravo AF: 0.456

Asia WGS AF: 0.241 AC: 840 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	11
DANN	Benign	0.81
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs6881634; hg19: chr5-77630854;