rs7755143

Positions:

• chr6-36965394-C-T

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 0.138 in 151,594 control chromosomes in the GnomAD database, including 1,569 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 0.14 (1569 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.386

ACMG classification

Verdict is Benign. Variant got -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 = 0.176 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20915 AN: 151508 Hom.: 1569 Cov.: 32

Gnomad AFR AF: 0.0848

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.0629

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.138 AC: 20915 AN: 151594 Hom.: 1569 Cov.: 32 AF XY: 0.139 AC XY: 10259 AN XY: 74060

Gnomad4 AFR AF: 0.0847

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.0633

Gnomad4 SAS AF: 0.167

Gnomad4 FIN AF: 0.154

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.104

Alfa AF: 0.155 Hom.: 983

Bravo AF: 0.137

Asia WGS AF: 0.132 AC: 460 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	0.79
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7755143; hg19: chr6-36933170;