rs2635556

Variant names:

• chr14-19944880-T-C
• rs2635556
• XR_007064055.1:n.49-1039A>G

Variant summary

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

The XR_007064055.1(LOC124903278):​n.49-1039A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 148,858 control chromosomes in the GnomAD database, including 4,698 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 0.31 (4698 hom., cov: 38)
• Consequence: LOC124903278 XR_007064055.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 2 publications found

Genes affected

LOC124903278 (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 (SAS) allele frequency at 95% confidence interval = 0.402 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: 0.307 AC: 45702 AN: 148734 Hom.: 4698 Cov.: 38

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.383

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.391

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.307 AC: 45707 AN: 148858 Hom.: 4698 Cov.: 38 AF XY: 0.308 AC XY: 22378 AN XY: 72740

African (AFR) AF: 0.109 AC: 4472 AN: 41178

American (AMR) AF: 0.325 AC: 4845 AN: 14894

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1389 AN: 3304

East Asian (EAS) AF: 0.226 AC: 1143 AN: 5052

South Asian (SAS) AF: 0.417 AC: 1939 AN: 4650

European-Finnish (FIN) AF: 0.398 AC: 4132 AN: 10392

Middle Eastern (MID) AF: 0.380 AC: 108 AN: 284

European-Non Finnish (NFE) AF: 0.403 AC: 26648 AN: 66184

Other (OTH) AF: 0.340 AC: 693 AN: 2038

Alfa AF: 0.345 Hom.: 633

Asia WGS AF: 0.340 AC: 1176 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.0
DANN	Benign	0.86
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2635556; hg19: chr14-20413039;