chr6-77560245-A-G

Variant names:

• chr6-77560245-A-G
• rs10943471

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 0.223 in 152,142 control chromosomes in the GnomAD database, including 4,190 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 0.22 (4190 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.53
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.472 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: 0.223 AC: 33846 AN: 152024 Hom.: 4189 Cov.: 32

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.487

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.223 AC: 33854 AN: 152142 Hom.: 4190 Cov.: 32 AF XY: 0.227 AC XY: 16901 AN XY: 74386

African (AFR) AF: 0.163 AC: 6770 AN: 41508

American (AMR) AF: 0.304 AC: 4640 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 738 AN: 3472

East Asian (EAS) AF: 0.488 AC: 2523 AN: 5170

South Asian (SAS) AF: 0.349 AC: 1682 AN: 4826

European-Finnish (FIN) AF: 0.190 AC: 2013 AN: 10596

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.215 AC: 14651 AN: 67990

Other (OTH) AF: 0.224 AC: 474 AN: 2114

Alfa AF: 0.222 Hom.: 673

Bravo AF: 0.226

Asia WGS AF: 0.402 AC: 1395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	10
DANN	Benign	0.75
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs10943471; hg19: chr6-78269962;