8-141726333-G-T

Variant names:

• chr8-141726333-G-T
• rs4072286
• XR_007061192.1:n.1734C>A

Variant summary

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

The XR_007061192.1(LOC124902074):​n.1734C>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 0.567 in 152,030 control chromosomes in the GnomAD database, including 25,481 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 0.57 (25481 hom., cov: 33)
• Consequence: LOC124902074 XR_007061192.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 7 publications found

Genes affected

LOC124902074 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.781 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902074	XR_007061192.1	n.1734C>A		non_coding_transcript_exon_variant	Exon 2 of 2
LOC124902074	XR_007061193.1	n.1403C>A		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297850	ENST00000751402.1	n.129-862G>T		intron_variant	Intron 1 of 1
ENSG00000297876	ENST00000751499.1	n.594+48C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.567 AC: 86193 AN: 151912 Hom.: 25476 Cov.: 33

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.520

Gnomad ASJ AF: 0.727

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.803

Gnomad FIN AF: 0.651

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.641

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.567 AC: 86225 AN: 152030 Hom.: 25481 Cov.: 33 AF XY: 0.573 AC XY: 42558 AN XY: 74304

African (AFR) AF: 0.409 AC: 16945 AN: 41438

American (AMR) AF: 0.520 AC: 7947 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.727 AC: 2522 AN: 3468

East Asian (EAS) AF: 0.480 AC: 2484 AN: 5170

South Asian (SAS) AF: 0.802 AC: 3855 AN: 4806

European-Finnish (FIN) AF: 0.651 AC: 6875 AN: 10564

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.641 AC: 43546 AN: 67974

Other (OTH) AF: 0.584 AC: 1234 AN: 2112

Alfa AF: 0.602 Hom.: 52305

Bravo AF: 0.544

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.18
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs4072286; hg19: chr8-142736531;