rs6696854

Variant names:

• chr1-161494024-T-C
• rs6696854
• XR_922214.3:n.1903+405T>C

Variant summary

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

The XR_922214.3(LOC105371473):​n.1903+405T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.738 in 152,012 control chromosomes in the GnomAD database, including 42,187 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 0.74 (42187 hom., cov: 31)
• Consequence: LOC105371473 XR_922214.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.20
• Publications: 19 publications found

Genes affected

LOC105371473 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.762 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: 0.738 AC: 112043 AN: 151894 Hom.: 42160 Cov.: 31

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.739

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.809

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.724

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.767

Gnomad OTH AF: 0.733

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

GnomAD4 genome AF: 0.738 AC: 112127 AN: 152012 Hom.: 42187 Cov.: 31 AF XY: 0.732 AC XY: 54393 AN XY: 74296

African (AFR) AF: 0.755 AC: 31258 AN: 41418

American (AMR) AF: 0.769 AC: 11761 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.809 AC: 2809 AN: 3472

East Asian (EAS) AF: 0.284 AC: 1468 AN: 5176

South Asian (SAS) AF: 0.540 AC: 2601 AN: 4814

European-Finnish (FIN) AF: 0.724 AC: 7648 AN: 10566

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.767 AC: 52140 AN: 67974

Other (OTH) AF: 0.730 AC: 1534 AN: 2102

Alfa AF: 0.755 Hom.: 185830

Bravo AF: 0.746

Asia WGS AF: 0.454 AC: 1585 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.17
DANN	Benign	0.14
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs6696854; hg19: chr1-161463814;