chr5-173506839-G-A

Variant names:

• chr5-173506839-G-A
• rs7716959
• ENST00000827042.1:n.446+467G>A

Variant summary

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

The ENST00000827042.1(ENSG00000253968):​n.446+467G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.366 in 151,842 control chromosomes in the GnomAD database, including 10,435 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 0.37 (10435 hom., cov: 31)
• Consequence: ENSG00000253968 ENST00000827042.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.290
• Publications: 2 publications found

Genes affected

ENSG00000253968 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377732	XR_001743001.1	n.2862+467G>A		intron_variant	Intron 13 of 14
LOC105377732	XR_007059057.1	n.3922+467G>A		intron_variant	Intron 16 of 17

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253968	ENST00000827042.1	n.446+467G>A		intron_variant	Intron 2 of 2
ENSG00000253968	ENST00000827044.1	n.374+467G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.366 AC: 55572 AN: 151724 Hom.: 10412 Cov.: 31

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.366 AC: 55641 AN: 151842 Hom.: 10435 Cov.: 31 AF XY: 0.370 AC XY: 27452 AN XY: 74220

African (AFR) AF: 0.294 AC: 12161 AN: 41384

American (AMR) AF: 0.464 AC: 7080 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1142 AN: 3470

East Asian (EAS) AF: 0.272 AC: 1401 AN: 5150

South Asian (SAS) AF: 0.403 AC: 1934 AN: 4798

European-Finnish (FIN) AF: 0.389 AC: 4108 AN: 10552

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.390 AC: 26499 AN: 67916

Other (OTH) AF: 0.394 AC: 831 AN: 2108

Alfa AF: 0.389 Hom.: 6526

Bravo AF: 0.368

Asia WGS AF: 0.347 AC: 1209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.7
DANN	Benign	0.73
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs7716959; hg19: chr5-172933842; COSMIC: COSV60232066;