6-78597647-G-A

Position:

• chr6-78597647-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0224 in 152,228 control chromosomes in the GnomAD database, including 62 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 0.022 (62 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0620

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0224 (3411/152228) while in subpopulation SAS AF= 0.0413 (199/4818). AF 95% confidence interval is 0.0366. There are 62 homozygotes in gnomad4. There are 1669 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 62 gene

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: 0.0224 AC: 3412 AN: 152110 Hom.: 62 Cov.: 33

Gnomad AFR AF: 0.00577

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0200

Gnomad ASJ AF: 0.0147

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0411

Gnomad FIN AF: 0.0190

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0347

Gnomad OTH AF: 0.0211

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

GnomAD4 genome AF: 0.0224 AC: 3411 AN: 152228 Hom.: 62 Cov.: 33 AF XY: 0.0224 AC XY: 1669 AN XY: 74428

Gnomad4 AFR AF: 0.00575

Gnomad4 AMR AF: 0.0199

Gnomad4 ASJ AF: 0.0147

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.0413

Gnomad4 FIN AF: 0.0190

Gnomad4 NFE AF: 0.0347

Gnomad4 OTH AF: 0.0208

Alfa AF: 0.0328 Hom.: 56

Bravo AF: 0.0217

Asia WGS AF: 0.0130 AC: 47 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	1.9
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10485131; hg19: chr6-79307364;