rs6734894

Variant names:

• chr2-6416649-G-A
• rs6734894
• XR_922743.1:n.133+2474C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_922743.1(LOC105373402):​n.133+2474C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,216 control chromosomes in the GnomAD database, including 1,073 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 0.11 (1073 hom., cov: 32)
• Consequence: LOC105373402 XR_922743.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.222

Genes affected

LOC105373402 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373402	XR_922743.1	n.133+2474C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16861 AN: 152098 Hom.: 1072 Cov.: 32

Gnomad AFR AF: 0.0959

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.0836

Gnomad ASJ AF: 0.0643

Gnomad EAS AF: 0.00694

Gnomad SAS AF: 0.0585

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.111 AC: 16869 AN: 152216 Hom.: 1073 Cov.: 32 AF XY: 0.107 AC XY: 7948 AN XY: 74426

Gnomad4 AFR AF: 0.0958

Gnomad4 AMR AF: 0.0834

Gnomad4 ASJ AF: 0.0643

Gnomad4 EAS AF: 0.00695

Gnomad4 SAS AF: 0.0590

Gnomad4 FIN AF: 0.103

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.103

Alfa AF: 0.126 Hom.: 695

Bravo AF: 0.109

Asia WGS AF: 0.0440 AC: 152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.22
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6734894; hg19: chr2-6556781;