6-41655295-G-T

Variant names:

• chr6-41655295-G-T
• rs2143678

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 0.186 in 140,220 control chromosomes in the GnomAD database, including 2,595 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 0.19 (2595 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.619

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.275 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: 0.186 AC: 25998 AN: 140148 Hom.: 2594 Cov.: 26

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.131

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.00467

Gnomad SAS AF: 0.0694

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.107

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.186 AC: 26014 AN: 140220 Hom.: 2595 Cov.: 26 AF XY: 0.186 AC XY: 12497 AN XY: 67134

Gnomad4 AFR AF: 0.280

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.122

Gnomad4 EAS AF: 0.00469

Gnomad4 SAS AF: 0.0692

Gnomad4 FIN AF: 0.200

Gnomad4 NFE AF: 0.164

Gnomad4 OTH AF: 0.159

Alfa AF: 0.157 Hom.: 4229

Bravo AF: 0.178

Asia WGS AF: 0.0630 AC: 218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.21
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2143678; hg19: chr6-41623033;