rs7837234

Variant names:

• chr8-63308096-G-T
• rs7837234
• XR_001745931.2:n.752+289G>T

Variant summary

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

The XR_001745931.2(LOC105375873):​n.752+289G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 151,898 control chromosomes in the GnomAD database, including 9,428 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 0.35 (9428 hom., cov: 31)
• Consequence: LOC105375873 XR_001745931.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.197
• Publications: 5 publications found

Genes affected

LOC105375873 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375873	XR_001745931.2	n.752+289G>T		intron_variant	Intron 4 of 5

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52470 AN: 151780 Hom.: 9409 Cov.: 31

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.0415

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.346 AC: 52536 AN: 151898 Hom.: 9428 Cov.: 31 AF XY: 0.341 AC XY: 25311 AN XY: 74228

African (AFR) AF: 0.355 AC: 14716 AN: 41412

American (AMR) AF: 0.334 AC: 5084 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.302 AC: 1046 AN: 3460

East Asian (EAS) AF: 0.0416 AC: 215 AN: 5170

South Asian (SAS) AF: 0.364 AC: 1749 AN: 4802

European-Finnish (FIN) AF: 0.308 AC: 3250 AN: 10544

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.372 AC: 25250 AN: 67952

Other (OTH) AF: 0.369 AC: 778 AN: 2108

Alfa AF: 0.364 Hom.: 43453

Bravo AF: 0.346

Asia WGS AF: 0.268 AC: 935 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.55
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs7837234; hg19: chr8-64220654;