rs72844411

Variant names:

• chr2-85496736-G-A
• rs72844411

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 0.193 in 152,110 control chromosomes in the GnomAD database, including 3,077 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 0.19 (3077 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.198

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.226 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: 0.193 AC: 29312 AN: 151992 Hom.: 3073 Cov.: 31

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.0392

Gnomad SAS AF: 0.0841

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.193 AC: 29342 AN: 152110 Hom.: 3077 Cov.: 31 AF XY: 0.191 AC XY: 14228 AN XY: 74350

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.180

Gnomad4 EAS AF: 0.0393

Gnomad4 SAS AF: 0.0852

Gnomad4 FIN AF: 0.293

Gnomad4 NFE AF: 0.229

Gnomad4 OTH AF: 0.201

Alfa AF: 0.205 Hom.: 398

Bravo AF: 0.183

Asia WGS AF: 0.0780 AC: 272 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	4.8
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs72844411; hg19: chr2-85723859; COSMIC: COSV71724935;