6-30796643-T-C

Variant names:

• chr6-30796643-T-C
• rs12660883

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 0.17 in 152,290 control chromosomes in the GnomAD database, including 3,016 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 0.17 (3016 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200
• Publications: 32 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 (SAS) allele frequency at 95% confidence interval = 0.366 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: 0.170 AC: 25826 AN: 152172 Hom.: 3009 Cov.: 32

Gnomad AFR AF: 0.0678

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.170 AC: 25839 AN: 152290 Hom.: 3016 Cov.: 32 AF XY: 0.176 AC XY: 13073 AN XY: 74470

African (AFR) AF: 0.0676 AC: 2812 AN: 41568

American (AMR) AF: 0.326 AC: 4982 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1381 AN: 3468

East Asian (EAS) AF: 0.323 AC: 1676 AN: 5192

South Asian (SAS) AF: 0.380 AC: 1837 AN: 4828

European-Finnish (FIN) AF: 0.114 AC: 1207 AN: 10612

Middle Eastern (MID) AF: 0.219 AC: 64 AN: 292

European-Non Finnish (NFE) AF: 0.164 AC: 11180 AN: 68024

Other (OTH) AF: 0.196 AC: 415 AN: 2114

Alfa AF: 0.176 Hom.: 8806

Bravo AF: 0.180

Asia WGS AF: 0.346 AC: 1204 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	2.2
DANN	Benign	0.72
PhyloP100		-0.0020

Splicing

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

Other links and lift over

dbSNP: rs12660883; hg19: chr6-30764420;