rs6475600

chr9-2203938-C-T

Variant summary

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

The XR_007061395.1(LOC107987043):n.302-22916G>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 0.309 in 151,878 control chromosomes in the GnomAD database, including 7,410 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 0.31 (7410 hom., cov: 32)
• Consequence: LOC107987043 XR_007061395.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.106

Genes affected

LOC107987043 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.403 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107987043	XR_007061395.1	n.302-22916G>A		intron_variant, non_coding_transcript_variant
LOC107987043	XR_001746600.2	n.298-22916G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46959 AN: 151760 Hom.: 7396 Cov.: 32

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.309 AC: 47002 AN: 151878 Hom.: 7410 Cov.: 32 AF XY: 0.310 AC XY: 22985 AN XY: 74208

Gnomad4 AFR AF: 0.341

Gnomad4 AMR AF: 0.326

Gnomad4 ASJ AF: 0.374

Gnomad4 EAS AF: 0.168

Gnomad4 SAS AF: 0.419

Gnomad4 FIN AF: 0.262

Gnomad4 NFE AF: 0.295

Gnomad4 OTH AF: 0.322

Alfa AF: 0.313 Hom.: 7094

Bravo AF: 0.314

Asia WGS AF: 0.310 AC: 1083 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.3
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6475600; hg19: chr9-2203938; COSMIC: COSV69634459;