XR_941720.2:n.200+1644T>C

Variant names:

• chr13-20322479-T-C
• rs7337231
• XR_941720.2:n.200+1644T>C

Variant summary

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

The XR_941720.2(LOC105370102):​n.200+1644T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 152,146 control chromosomes in the GnomAD database, including 13,798 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 0.40 (13798 hom., cov: 32)
• Consequence: LOC105370102 XR_941720.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 4 publications found

Genes affected

LOC105370102 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.401 AC: 61025 AN: 152028 Hom.: 13788 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.401 AC: 61075 AN: 152146 Hom.: 13798 Cov.: 32 AF XY: 0.399 AC XY: 29675 AN XY: 74372

African (AFR) AF: 0.194 AC: 8048 AN: 41548

American (AMR) AF: 0.434 AC: 6633 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 1203 AN: 3470

East Asian (EAS) AF: 0.248 AC: 1287 AN: 5188

South Asian (SAS) AF: 0.441 AC: 2128 AN: 4824

European-Finnish (FIN) AF: 0.493 AC: 5205 AN: 10564

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.516 AC: 35053 AN: 67962

Other (OTH) AF: 0.413 AC: 869 AN: 2106

Alfa AF: 0.481 Hom.: 47513

Bravo AF: 0.386

Asia WGS AF: 0.408 AC: 1421 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.052
DANN	Benign	0.54
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs7337231; hg19: chr13-20896618;