rs12644119

Variant names:

• chr4-89682268-C-A
• rs12644119
• XR_001741764.2:n.764C>A

Your query was ambiguous. Multiple possible variants found:

• chr4-89682268-C-A
• chr4-89682268-C-G
• chr4-89682268-C-T

Variant summary

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

The XR_001741764.2(LOC124900602):​n.764C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 151,780 control chromosomes in the GnomAD database, including 3,213 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 0.18 (3213 hom., cov: 32)
• Consequence: LOC124900602 XR_001741764.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.601
• Publications: 12 publications found

Genes affected

LOC124900602 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900602	XR_001741764.2	n.764C>A		non_coding_transcript_exon_variant	Exon 1 of 3
LOC124900602	XR_007058465.1	n.764C>A		non_coding_transcript_exon_variant	Exon 1 of 2
LOC124900602	XR_007058466.1	n.764C>A		non_coding_transcript_exon_variant	Exon 1 of 3
LOC124900602	XR_938983.2	n.764C>A		non_coding_transcript_exon_variant	Exon 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000251095	ENST00000506864.5	n.472-9017C>A		intron_variant	Intron 3 of 3	4
ENSG00000251095	ENST00000507916.6	n.135-9017C>A		intron_variant	Intron 1 of 2	3
ENSG00000251095	ENST00000508021.5	n.327-9017C>A		intron_variant	Intron 3 of 4	4

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26916 AN: 151660 Hom.: 3198 Cov.: 32

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.0606

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.178 AC: 26976 AN: 151780 Hom.: 3213 Cov.: 32 AF XY: 0.181 AC XY: 13438 AN XY: 74174

African (AFR) AF: 0.275 AC: 11395 AN: 41376

American (AMR) AF: 0.162 AC: 2472 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 636 AN: 3470

East Asian (EAS) AF: 0.517 AC: 2664 AN: 5150

South Asian (SAS) AF: 0.234 AC: 1126 AN: 4822

European-Finnish (FIN) AF: 0.120 AC: 1256 AN: 10496

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.102 AC: 6924 AN: 67916

Other (OTH) AF: 0.183 AC: 386 AN: 2108

Alfa AF: 0.119 Hom.: 2293

Bravo AF: 0.186

Asia WGS AF: 0.381 AC: 1319 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.83
DANN	Benign	0.14
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs12644119; hg19: chr4-90603419;