6-109945212-A-T

Variant names:

• chr6-109945212-A-T
• rs2503770

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.785

Gnomad4 AMR AF: 0.474

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.902

Gnomad4 SAS AF: 0.591

Gnomad4 FIN AF: 0.346

Gnomad4 NFE AF: 0.235

Gnomad4 OTH AF: 0.421

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

Splicing

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

Publications

LitVar

Other links and lift over

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