chr6-6337273-C-T

Variant names:

• chr6-6337273-C-T
• rs11243081

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 0.23 in 152,162 control chromosomes in the GnomAD database, including 5,080 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 0.23 (5080 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0240
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.395 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: 0.230 AC: 35031 AN: 152046 Hom.: 5085 Cov.: 33

Gnomad AFR AF: 0.0631

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.230 AC: 35006 AN: 152162 Hom.: 5080 Cov.: 33 AF XY: 0.228 AC XY: 16951 AN XY: 74390

African (AFR) AF: 0.0629 AC: 2614 AN: 41544

American (AMR) AF: 0.191 AC: 2914 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 801 AN: 3470

East Asian (EAS) AF: 0.410 AC: 2123 AN: 5180

South Asian (SAS) AF: 0.257 AC: 1236 AN: 4816

European-Finnish (FIN) AF: 0.263 AC: 2782 AN: 10568

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.319 AC: 21662 AN: 67996

Other (OTH) AF: 0.237 AC: 501 AN: 2112

Alfa AF: 0.291 Hom.: 29860

Bravo AF: 0.220

Asia WGS AF: 0.300 AC: 1040 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.2
DANN	Benign	0.48
PhyloP100		-0.024

Splicing

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

Other links and lift over

dbSNP: rs11243081; hg19: chr6-6337506;