rs639370

chr6-78691696-T-C

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 0.639 in 152,048 control chromosomes in the GnomAD database, including 31,473 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 0.64 (31473 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.434

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.691 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.640 AC: 97173 AN: 151930 Hom.: 31468 Cov.: 32

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.487

Gnomad SAS AF: 0.618

Gnomad FIN AF: 0.710

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.648

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

GnomAD4 genome AF: 0.639 AC: 97212 AN: 152048 Hom.: 31473 Cov.: 32 AF XY: 0.639 AC XY: 47496 AN XY: 74318

Gnomad4 AFR AF: 0.568

Gnomad4 AMR AF: 0.593

Gnomad4 ASJ AF: 0.636

Gnomad4 EAS AF: 0.488

Gnomad4 SAS AF: 0.618

Gnomad4 FIN AF: 0.710

Gnomad4 NFE AF: 0.696

Gnomad4 OTH AF: 0.645

Alfa AF: 0.672 Hom.: 53702

Bravo AF: 0.629

Asia WGS AF: 0.526 AC: 1824 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	2.4
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs639370; hg19: chr6-79401413;