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_007062909.1(LOC105369519):​n.251+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_007062909.1 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369519	XR_007062909.1	n.251+3662T>C		intron_variant	Intron 2 of 3
LOC105369519	XR_007062910.1	n.205+3662T>C		intron_variant	Intron 2 of 3
LOC105369519	XR_948068.3	n.342+3662T>C		intron_variant	Intron 2 of 3
LOC105369519	XR_948069.3	n.253+3662T>C		intron_variant	Intron 2 of 3

Ensembl

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

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 v4.3

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;