rs6734894

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

Genes affected

LOC105373402 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

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

African (AFR) AF: 0.0958 AC: 3979 AN: 41532

American (AMR) AF: 0.0834 AC: 1275 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0643 AC: 223 AN: 3470

East Asian (EAS) AF: 0.00695 AC: 36 AN: 5178

South Asian (SAS) AF: 0.0590 AC: 285 AN: 4830

European-Finnish (FIN) AF: 0.103 AC: 1087 AN: 10600

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.142 AC: 9653 AN: 68002

Other (OTH) AF: 0.103 AC: 217 AN: 2110

Alfa AF: 0.127 Hom.: 2529

Bravo AF: 0.109

Asia WGS AF: 0.0440 AC: 152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.22
DANN	Benign	0.50
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs6734894; hg19: chr2-6556781;