6-109945212-A-T

Variant names:

• chr6-109945212-A-T
• rs2503770

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 0.455 in 152,034 control chromosomes in the GnomAD database, including 20,530 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 0.46 (20530 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00500
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.88 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: 0.455 AC: 69059 AN: 151916 Hom.: 20475 Cov.: 32

Gnomad AFR AF: 0.784

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.901

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.455 AC: 69179 AN: 152034 Hom.: 20530 Cov.: 32 AF XY: 0.466 AC XY: 34637 AN XY: 74320

African (AFR) AF: 0.785 AC: 32527 AN: 41460

American (AMR) AF: 0.474 AC: 7247 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 993 AN: 3468

East Asian (EAS) AF: 0.902 AC: 4663 AN: 5172

South Asian (SAS) AF: 0.591 AC: 2844 AN: 4814

European-Finnish (FIN) AF: 0.346 AC: 3652 AN: 10552

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.235 AC: 15945 AN: 67976

Other (OTH) AF: 0.421 AC: 887 AN: 2106

Alfa AF: 0.345 Hom.: 1563

Bravo AF: 0.478

Asia WGS AF: 0.732 AC: 2545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.8
DANN	Benign	0.82
PhyloP100		0.0050

Splicing

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

Other links and lift over

dbSNP: rs2503770; hg19: chr6-110266415; COSMIC: COSV60265529;