rs1341446

Variant names:

• chr1-241378588-G-A
• rs1341446

Your query was ambiguous. Multiple possible variants found:

• chr1-241378588-G-A
• chr1-241378588-G-C
• chr1-241378588-G-T

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 0.526 in 151,974 control chromosomes in the GnomAD database, including 21,165 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 0.53 (21165 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.128

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.588 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: 0.526 AC: 79871 AN: 151856 Hom.: 21140 Cov.: 32

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.692

Gnomad AMR AF: 0.552

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.526 AC: 79939 AN: 151974 Hom.: 21165 Cov.: 32 AF XY: 0.527 AC XY: 39127 AN XY: 74256

Gnomad4 AFR AF: 0.558

Gnomad4 AMR AF: 0.552

Gnomad4 ASJ AF: 0.514

Gnomad4 EAS AF: 0.606

Gnomad4 SAS AF: 0.549

Gnomad4 FIN AF: 0.501

Gnomad4 NFE AF: 0.496

Gnomad4 OTH AF: 0.528

Alfa AF: 0.481 Hom.: 7934

Bravo AF: 0.532

Asia WGS AF: 0.580 AC: 2018 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1341446; hg19: chr1-241541888;