chr1-34624472-T-C

Variant names:

• chr1-34624472-T-C
• rs2359631
• XR_001737964.2:n.156-8777A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001737964.2(LOC105378641):​n.156-8777A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.533 in 152,034 control chromosomes in the GnomAD database, including 21,783 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 (21783 hom., cov: 32)
• Consequence: LOC105378641 XR_001737964.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 1 publications found

Genes affected

LOC105378641 (HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.545 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.533 AC: 80899 AN: 151916 Hom.: 21755 Cov.: 32

Gnomad AFR AF: 0.533

Gnomad AMI AF: 0.811

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.533 AC: 80983 AN: 152034 Hom.: 21783 Cov.: 32 AF XY: 0.533 AC XY: 39627 AN XY: 74320

African (AFR) AF: 0.533 AC: 22111 AN: 41452

American (AMR) AF: 0.497 AC: 7606 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.542 AC: 1883 AN: 3472

East Asian (EAS) AF: 0.329 AC: 1701 AN: 5176

South Asian (SAS) AF: 0.531 AC: 2556 AN: 4810

European-Finnish (FIN) AF: 0.548 AC: 5774 AN: 10542

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.549 AC: 37333 AN: 67976

Other (OTH) AF: 0.532 AC: 1122 AN: 2108

Alfa AF: 0.543 Hom.: 11991

Bravo AF: 0.528

Asia WGS AF: 0.481 AC: 1674 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.80
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2359631; hg19: chr1-35090073; COSMIC: COSV59937411;