rs503897

chr9-37382102-G-Achr9-37382102-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007061478.1(LOC124902153):n.4376-75G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.689 in 152,052 control chromosomes in the GnomAD database, including 37,095 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 (37095 hom., cov: 32)
• Consequence: LOC124902153 XR_007061478.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.229

Genes affected

LOC124902153 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902153	XR_007061478.1	n.4376-75G>A		intron_variant, non_coding_transcript_variant
LOC124902153	XR_007061477.1	n.680G>A		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.689 AC: 104712 AN: 151934 Hom.: 37059 Cov.: 32

Gnomad AFR AF: 0.837

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.629

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.584

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.655

Gnomad OTH AF: 0.652

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

GnomAD4 genome AF: 0.689 AC: 104800 AN: 152052 Hom.: 37095 Cov.: 32 AF XY: 0.683 AC XY: 50705 AN XY: 74288

Gnomad4 AFR AF: 0.837

Gnomad4 AMR AF: 0.707

Gnomad4 ASJ AF: 0.629

Gnomad4 EAS AF: 0.345

Gnomad4 SAS AF: 0.527

Gnomad4 FIN AF: 0.584

Gnomad4 NFE AF: 0.655

Gnomad4 OTH AF: 0.644

Alfa AF: 0.653 Hom.: 65076

Bravo AF: 0.706

Asia WGS AF: 0.493 AC: 1717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	1.4
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs503897; hg19: chr9-37382099; COSMIC: COSV71913238;