rs644498

Variant names:

• chr11-118696777-T-C
• rs644498
• XR_007062909.1:n.251+3662T>C

Your query was ambiguous. Multiple possible variants found:

• chr11-118696777-T-C
• chr11-118696777-T-G

Variant summary

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

The XR_948068.3(LOC105369519):​n.342+3662T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 152,112 control chromosomes in the GnomAD database, including 8,298 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 0.32 (8298 hom., cov: 32)
• Consequence: LOC105369519 XR_948068.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0710
• Publications: 10 publications found

Genes affected

LOC105369519 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.453 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: 0.323 AC: 49159 AN: 151994 Hom.: 8282 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.323 AC: 49198 AN: 152112 Hom.: 8298 Cov.: 32 AF XY: 0.324 AC XY: 24073 AN XY: 74384

African (AFR) AF: 0.266 AC: 11049 AN: 41500

American (AMR) AF: 0.462 AC: 7057 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1259 AN: 3470

East Asian (EAS) AF: 0.405 AC: 2091 AN: 5162

South Asian (SAS) AF: 0.199 AC: 959 AN: 4826

European-Finnish (FIN) AF: 0.312 AC: 3306 AN: 10592

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.327 AC: 22224 AN: 67982

Other (OTH) AF: 0.335 AC: 709 AN: 2114

Alfa AF: 0.331 Hom.: 1061

Bravo AF: 0.340

Asia WGS AF: 0.278 AC: 969 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.4
DANN	Benign	0.60
PhyloP100		-0.071

Splicing

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

Other links and lift over

dbSNP: rs644498; hg19: chr11-118567486;