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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903278	XR_007064055.1	n.49-1039A>G		intron_variant	Intron 1 of 3

Ensembl

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

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 v4.3

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;