rs4949238

Variant names:

• chr1-29949749-A-G
• rs4949238

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 0.195 in 152,168 control chromosomes in the GnomAD database, including 3,329 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 (3329 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.127
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.314 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: 0.195 AC: 29590 AN: 152050 Hom.: 3325 Cov.: 32

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.0763

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.195 AC: 29622 AN: 152168 Hom.: 3329 Cov.: 32 AF XY: 0.194 AC XY: 14449 AN XY: 74396

African (AFR) AF: 0.319 AC: 13223 AN: 41492

American (AMR) AF: 0.165 AC: 2530 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.133 AC: 462 AN: 3472

East Asian (EAS) AF: 0.0763 AC: 395 AN: 5176

South Asian (SAS) AF: 0.121 AC: 583 AN: 4822

European-Finnish (FIN) AF: 0.193 AC: 2042 AN: 10594

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.144 AC: 9802 AN: 68004

Other (OTH) AF: 0.183 AC: 387 AN: 2114

Alfa AF: 0.157 Hom.: 9045

Bravo AF: 0.202

Asia WGS AF: 0.125 AC: 436 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.1
DANN	Benign	0.70
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs4949238; hg19: chr1-30422596;