6-75233353-T-G

Variant names:

• chr6-75233353-T-G
• rs1203213

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 0.893 in 152,194 control chromosomes in the GnomAD database, including 61,146 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 0.89 (61146 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.116
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.942 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: 0.893 AC: 135878 AN: 152076 Hom.: 61119 Cov.: 31

Gnomad AFR AF: 0.775

Gnomad AMI AF: 0.948

Gnomad AMR AF: 0.936

Gnomad ASJ AF: 0.906

Gnomad EAS AF: 0.860

Gnomad SAS AF: 0.882

Gnomad FIN AF: 0.955

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.948

Gnomad OTH AF: 0.911

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

GnomAD4 genome AF: 0.893 AC: 135959 AN: 152194 Hom.: 61146 Cov.: 31 AF XY: 0.893 AC XY: 66482 AN XY: 74424

African (AFR) AF: 0.775 AC: 32136 AN: 41488

American (AMR) AF: 0.935 AC: 14300 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.906 AC: 3144 AN: 3470

East Asian (EAS) AF: 0.860 AC: 4443 AN: 5166

South Asian (SAS) AF: 0.882 AC: 4253 AN: 4820

European-Finnish (FIN) AF: 0.955 AC: 10133 AN: 10614

Middle Eastern (MID) AF: 0.895 AC: 263 AN: 294

European-Non Finnish (NFE) AF: 0.948 AC: 64495 AN: 68032

Other (OTH) AF: 0.912 AC: 1927 AN: 2112

Alfa AF: 0.923 Hom.: 25507

Bravo AF: 0.887

Asia WGS AF: 0.847 AC: 2946 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	0.81
DANN	Benign	0.37
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs1203213; hg19: chr6-75943069;