rs1431659

Variant names:

• chr8-72526835-A-G
• rs1431659
• XR_929042.3:n.797+4715T>C

Variant summary

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

The XR_929042.3(LOC105375897):​n.797+4715T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.738 in 151,994 control chromosomes in the GnomAD database, including 41,518 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 0.74 (41518 hom., cov: 31)
• Consequence: LOC105375897 XR_929042.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.951
• Publications: 10 publications found

Genes affected

LOC105375897 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.78 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375897	XR_929042.3	n.797+4715T>C		intron_variant	Intron 2 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.738 AC: 112127 AN: 151876 Hom.: 41476 Cov.: 31

Gnomad AFR AF: 0.741

Gnomad AMI AF: 0.808

Gnomad AMR AF: 0.792

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.764

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.731

Gnomad OTH AF: 0.730

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

GnomAD4 genome AF: 0.738 AC: 112222 AN: 151994 Hom.: 41518 Cov.: 31 AF XY: 0.740 AC XY: 54917 AN XY: 74262

African (AFR) AF: 0.741 AC: 30698 AN: 41444

American (AMR) AF: 0.792 AC: 12088 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.733 AC: 2539 AN: 3466

East Asian (EAS) AF: 0.696 AC: 3588 AN: 5154

South Asian (SAS) AF: 0.645 AC: 3102 AN: 4808

European-Finnish (FIN) AF: 0.764 AC: 8077 AN: 10576

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.731 AC: 49679 AN: 67964

Other (OTH) AF: 0.727 AC: 1537 AN: 2114

Alfa AF: 0.744 Hom.: 7336

Bravo AF: 0.744

Asia WGS AF: 0.714 AC: 2482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.74
DANN	Benign	0.32
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs1431659; hg19: chr8-73439070;