chr6-36965394-C-T

Variant names:

• chr6-36965394-C-T
• rs7755143

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 0.138 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
• Publications: 13 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 = 0.176 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: 0.138 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

African (AFR) AF: 0.0847 AC: 3493 AN: 41226

American (AMR) AF: 0.182 AC: 2769 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 395 AN: 3472

East Asian (EAS) AF: 0.0633 AC: 327 AN: 5168

South Asian (SAS) AF: 0.167 AC: 802 AN: 4812

European-Finnish (FIN) AF: 0.154 AC: 1609 AN: 10450

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10940 AN: 67924

Other (OTH) AF: 0.104 AC: 218 AN: 2100

Alfa AF: 0.151 Hom.: 1335

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
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs7755143; hg19: chr6-36933170;