6-130810794-C-T

Variant names:

• chr6-130810794-C-T
• rs7744295

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 0.165 in 152,164 control chromosomes in the GnomAD database, including 2,154 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 0.17 (2154 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.845
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.218 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: 0.165 AC: 25134 AN: 152046 Hom.: 2147 Cov.: 32

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.0771

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.165 AC: 25149 AN: 152164 Hom.: 2154 Cov.: 32 AF XY: 0.164 AC XY: 12215 AN XY: 74392

African (AFR) AF: 0.184 AC: 7621 AN: 41504

American (AMR) AF: 0.224 AC: 3422 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 477 AN: 3470

East Asian (EAS) AF: 0.0769 AC: 398 AN: 5178

South Asian (SAS) AF: 0.145 AC: 700 AN: 4832

European-Finnish (FIN) AF: 0.113 AC: 1193 AN: 10586

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.159 AC: 10785 AN: 68000

Other (OTH) AF: 0.168 AC: 355 AN: 2110

Alfa AF: 0.160 Hom.: 6590

Bravo AF: 0.175

Asia WGS AF: 0.109 AC: 380 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.14
DANN	Benign	0.72
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs7744295; hg19: chr6-131131934;