9-87058705-C-T

Variant names:

• chr9-87058705-C-T
• rs1350564
• XR_007061638.1:n.124+5295C>T

Variant summary

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

The XR_007061638.1(LOC124902196):​n.124+5295C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.497 in 152,002 control chromosomes in the GnomAD database, including 19,532 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 0.50 (19532 hom., cov: 32)
• Consequence: LOC124902196 XR_007061638.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.631
• Publications: 2 publications found

Genes affected

LOC124902196 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.702 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902196	XR_007061638.1	n.124+5295C>T		intron_variant	Intron 1 of 1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.497 AC: 75511 AN: 151884 Hom.: 19525 Cov.: 32

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.497 AC: 75537 AN: 152002 Hom.: 19532 Cov.: 32 AF XY: 0.496 AC XY: 36850 AN XY: 74316

African (AFR) AF: 0.346 AC: 14355 AN: 41444

American (AMR) AF: 0.607 AC: 9270 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.542 AC: 1881 AN: 3472

East Asian (EAS) AF: 0.721 AC: 3714 AN: 5150

South Asian (SAS) AF: 0.526 AC: 2532 AN: 4816

European-Finnish (FIN) AF: 0.480 AC: 5076 AN: 10574

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.542 AC: 36830 AN: 67974

Other (OTH) AF: 0.541 AC: 1138 AN: 2104

Alfa AF: 0.524 Hom.: 10815

Bravo AF: 0.503

Asia WGS AF: 0.602 AC: 2093 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.2
DANN	Benign	0.51
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs1350564; hg19: chr9-89673620;