chr1-241523216-A-G

Variant names:

• chr1-241523216-A-G
• rs1414493

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 0.624 in 151,728 control chromosomes in the GnomAD database, including 30,560 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 0.62 (30560 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.718 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: 0.624 AC: 94674 AN: 151610 Hom.: 30546 Cov.: 30

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.776

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.736

Gnomad FIN AF: 0.742

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.709

Gnomad OTH AF: 0.608

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

GnomAD4 genome AF: 0.624 AC: 94722 AN: 151728 Hom.: 30560 Cov.: 30 AF XY: 0.627 AC XY: 46472 AN XY: 74168

Gnomad4 AFR AF: 0.467

Gnomad4 AMR AF: 0.614

Gnomad4 ASJ AF: 0.639

Gnomad4 EAS AF: 0.429

Gnomad4 SAS AF: 0.738

Gnomad4 FIN AF: 0.742

Gnomad4 NFE AF: 0.709

Gnomad4 OTH AF: 0.609

Alfa AF: 0.662 Hom.: 10030

Bravo AF: 0.598

Asia WGS AF: 0.586 AC: 2036 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.5
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1414493; hg19: chr1-241686516;