chr1-203208953-G-A

Variant names:

• chr1-203208953-G-A
• rs4950934

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 0.0879 in 152,272 control chromosomes in the GnomAD database, including 909 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 0.088 (909 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.149
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.271 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: 0.0879 AC: 13379 AN: 152154 Hom.: 908 Cov.: 33

Gnomad AFR AF: 0.0205

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.0409

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.0879 AC: 13385 AN: 152272 Hom.: 909 Cov.: 33 AF XY: 0.0920 AC XY: 6850 AN XY: 74454

African (AFR) AF: 0.0204 AC: 848 AN: 41570

American (AMR) AF: 0.117 AC: 1784 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 505 AN: 3468

East Asian (EAS) AF: 0.242 AC: 1255 AN: 5190

South Asian (SAS) AF: 0.284 AC: 1369 AN: 4828

European-Finnish (FIN) AF: 0.0409 AC: 433 AN: 10598

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6851 AN: 68006

Other (OTH) AF: 0.114 AC: 241 AN: 2116

Alfa AF: 0.0821 Hom.: 430

Bravo AF: 0.0872

Asia WGS AF: 0.234 AC: 810 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.2
DANN	Benign	0.67
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs4950934; hg19: chr1-203178081;