chr1-241895919-G-A

Variant names:

• chr1-241895919-G-A
• rs4658535

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 0.241 in 151,962 control chromosomes in the GnomAD database, including 5,066 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 0.24 (5066 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.238
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.562 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: 0.241 AC: 36583 AN: 151842 Hom.: 5061 Cov.: 32

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.580

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.241 AC: 36635 AN: 151962 Hom.: 5066 Cov.: 32 AF XY: 0.246 AC XY: 18296 AN XY: 74284

African (AFR) AF: 0.288 AC: 11913 AN: 41424

American (AMR) AF: 0.336 AC: 5125 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 575 AN: 3468

East Asian (EAS) AF: 0.580 AC: 2994 AN: 5166

South Asian (SAS) AF: 0.243 AC: 1168 AN: 4816

European-Finnish (FIN) AF: 0.153 AC: 1613 AN: 10550

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.183 AC: 12413 AN: 67962

Other (OTH) AF: 0.245 AC: 518 AN: 2110

Alfa AF: 0.207 Hom.: 15808

Bravo AF: 0.262

Asia WGS AF: 0.392 AC: 1363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.5
DANN	Benign	0.58
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs4658535; hg19: chr1-242059221;