rs2745636

Variant names:

• chr6-1448886-G-T
• rs2745636

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 0.53 in 152,034 control chromosomes in the GnomAD database, including 21,786 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 0.53 (21786 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.644 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: 0.530 AC: 80567 AN: 151916 Hom.: 21776 Cov.: 33

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.663

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.497

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

GnomAD4 genome AF: 0.530 AC: 80617 AN: 152034 Hom.: 21786 Cov.: 33 AF XY: 0.533 AC XY: 39573 AN XY: 74290

Gnomad4 AFR AF: 0.461

Gnomad4 AMR AF: 0.641

Gnomad4 ASJ AF: 0.401

Gnomad4 EAS AF: 0.663

Gnomad4 SAS AF: 0.608

Gnomad4 FIN AF: 0.492

Gnomad4 NFE AF: 0.548

Gnomad4 OTH AF: 0.494

Alfa AF: 0.537 Hom.: 32687

Bravo AF: 0.537

Asia WGS AF: 0.615 AC: 2138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2745636; hg19: chr6-1449121;