9-108133073-C-T

Variant names:

• chr9-108133073-C-T
• rs676256
• XR_001746881.2:n.721-79779G>A

Variant summary

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

The XR_001746881.2(LOC105376214):​n.721-79779G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.686 in 152,056 control chromosomes in the GnomAD database, including 36,294 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 0.69 (36294 hom., cov: 32)
• Consequence: LOC105376214 XR_001746881.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.32
• Publications: 16 publications found

Genes affected

LOC105376214 (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 = 0.934 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376214	XR_001746881.2	n.721-79779G>A		intron_variant	Intron 4 of 4
LOC105376214	XR_001746882.2	n.721-79779G>A		intron_variant	Intron 4 of 5
LOC105376214	XR_007061722.1	n.721-79779G>A		intron_variant	Intron 4 of 5

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.686 AC: 104263 AN: 151938 Hom.: 36236 Cov.: 32

Gnomad AFR AF: 0.752

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.957

Gnomad SAS AF: 0.856

Gnomad FIN AF: 0.659

Gnomad MID AF: 0.653

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.679

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

GnomAD4 genome AF: 0.686 AC: 104382 AN: 152056 Hom.: 36294 Cov.: 32 AF XY: 0.695 AC XY: 51637 AN XY: 74316

African (AFR) AF: 0.753 AC: 31253 AN: 41510

American (AMR) AF: 0.668 AC: 10207 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.636 AC: 2208 AN: 3470

East Asian (EAS) AF: 0.957 AC: 4942 AN: 5166

South Asian (SAS) AF: 0.855 AC: 4129 AN: 4828

European-Finnish (FIN) AF: 0.659 AC: 6938 AN: 10536

Middle Eastern (MID) AF: 0.664 AC: 194 AN: 292

European-Non Finnish (NFE) AF: 0.625 AC: 42490 AN: 67968

Other (OTH) AF: 0.682 AC: 1438 AN: 2110

Alfa AF: 0.647 Hom.: 53768

Bravo AF: 0.688

Asia WGS AF: 0.893 AC: 3099 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.018
DANN	Benign	0.71
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs676256; hg19: chr9-110895353; COSMIC: COSV60390074;