XR_002956872.2:n.357-64469A>T

Variant names:

• chr9-1399674-A-T
• rs6474795
• XR_002956872.2:n.357-64469A>T

Variant summary

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

The XR_002956872.2(LOC102723803):​n.357-64469A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 152,038 control chromosomes in the GnomAD database, including 9,259 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 0.30 (9259 hom., cov: 32)
• Consequence: LOC102723803 XR_002956872.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.160
• Publications: 4 publications found

Genes affected

LOC102723803 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.576 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723803	XR_002956872.2	n.357-64469A>T		intron_variant	Intron 3 of 7
LOC102723803	XR_929415.3	n.357-64469A>T		intron_variant	Intron 3 of 6

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45637 AN: 151920 Hom.: 9213 Cov.: 32

Gnomad AFR AF: 0.582

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.0836

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.301 AC: 45730 AN: 152038 Hom.: 9259 Cov.: 32 AF XY: 0.294 AC XY: 21842 AN XY: 74328

African (AFR) AF: 0.582 AC: 24139 AN: 41456

American (AMR) AF: 0.169 AC: 2581 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 762 AN: 3470

East Asian (EAS) AF: 0.0828 AC: 429 AN: 5182

South Asian (SAS) AF: 0.141 AC: 677 AN: 4808

European-Finnish (FIN) AF: 0.200 AC: 2114 AN: 10580

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.210 AC: 14249 AN: 67960

Other (OTH) AF: 0.264 AC: 557 AN: 2112

Alfa AF: 0.190 Hom.: 1657

Bravo AF: 0.309

Asia WGS AF: 0.149 AC: 520 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.8
DANN	Benign	0.78
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs6474795; hg19: chr9-1399674; COSMIC: COSV69440299;