rs1440095

Variant names:

• chr2-42062526-T-C
• rs1440095

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 0.454 in 152,034 control chromosomes in the GnomAD database, including 16,359 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 0.45 (16359 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.567 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: 0.454 AC: 68914 AN: 151916 Hom.: 16317 Cov.: 32

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.454 AC: 69018 AN: 152034 Hom.: 16359 Cov.: 32 AF XY: 0.456 AC XY: 33894 AN XY: 74310

African (AFR) AF: 0.573 AC: 23756 AN: 41434

American (AMR) AF: 0.537 AC: 8215 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.431 AC: 1494 AN: 3470

East Asian (EAS) AF: 0.497 AC: 2556 AN: 5144

South Asian (SAS) AF: 0.434 AC: 2090 AN: 4814

European-Finnish (FIN) AF: 0.391 AC: 4132 AN: 10570

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.370 AC: 25167 AN: 67998

Other (OTH) AF: 0.440 AC: 928 AN: 2110

Alfa AF: 0.401 Hom.: 47704

Bravo AF: 0.475

Asia WGS AF: 0.488 AC: 1694 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.7
DANN	Benign	0.85
PhyloP100		0.0090

Splicing

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

Other links and lift over

dbSNP: rs1440095; hg19: chr2-42289666;