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. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.558 AC: 23095 AN: 41418

American (AMR) AF: 0.552 AC: 8440 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.514 AC: 1782 AN: 3464

East Asian (EAS) AF: 0.606 AC: 3125 AN: 5158

South Asian (SAS) AF: 0.549 AC: 2643 AN: 4816

European-Finnish (FIN) AF: 0.501 AC: 5282 AN: 10546

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.496 AC: 33688 AN: 67978

Other (OTH) AF: 0.528 AC: 1113 AN: 2108

Alfa AF: 0.491 Hom.: 12214

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
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs1341446; hg19: chr1-241541888;