chr2-44096945-C-T

Variant names:

• chr2-44096945-C-T
• rs6757201

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 0.417 in 152,102 control chromosomes in the GnomAD database, including 15,294 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 0.42 (15294 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.658 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: 0.416 AC: 63292 AN: 151984 Hom.: 15265 Cov.: 32

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.417 AC: 63370 AN: 152102 Hom.: 15294 Cov.: 32 AF XY: 0.410 AC XY: 30466 AN XY: 74364

African (AFR) AF: 0.664 AC: 27537 AN: 41462

American (AMR) AF: 0.321 AC: 4903 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1228 AN: 3472

East Asian (EAS) AF: 0.453 AC: 2349 AN: 5184

South Asian (SAS) AF: 0.409 AC: 1972 AN: 4820

European-Finnish (FIN) AF: 0.225 AC: 2380 AN: 10588

Middle Eastern (MID) AF: 0.432 AC: 126 AN: 292

European-Non Finnish (NFE) AF: 0.322 AC: 21875 AN: 67970

Other (OTH) AF: 0.422 AC: 893 AN: 2114

Alfa AF: 0.360 Hom.: 6624

Bravo AF: 0.435

Asia WGS AF: 0.439 AC: 1529 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.37
DANN	Benign	0.88
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs6757201; hg19: chr2-44324084;