rs974448

Variant names:

• chr2-222140595-A-G
• rs974448

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 0.16 in 152,076 control chromosomes in the GnomAD database, including 2,074 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 0.16 (2074 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0250

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.17 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: 0.161 AC: 24404 AN: 151958 Hom.: 2074 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.0643

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.160 AC: 24406 AN: 152076 Hom.: 2074 Cov.: 32 AF XY: 0.160 AC XY: 11909 AN XY: 74334

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.281

Gnomad4 EAS AF: 0.0645

Gnomad4 SAS AF: 0.145

Gnomad4 FIN AF: 0.154

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.189

Alfa AF: 0.161 Hom.: 262

Bravo AF: 0.161

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.0
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs974448; hg19: chr2-223005314;