chr9-74126500-G-C

Position:

• chr9-74126500-G-C

Variant summary

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

The XR_242624.4(LOC101927329):​n.686-2600C>G 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 0.206 in 152,034 control chromosomes in the GnomAD database, including 3,964 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 0.21 (3964 hom., cov: 32)
• Consequence: LOC101927329 XR_242624.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.106

Genes affected

LOC101927329 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927329	XR_242624.4	n.686-2600C>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31387 AN: 151916 Hom.: 3970 Cov.: 32

Gnomad AFR AF: 0.0750

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.206 AC: 31381 AN: 152034 Hom.: 3964 Cov.: 32 AF XY: 0.210 AC XY: 15603 AN XY: 74290

Gnomad4 AFR AF: 0.0750

Gnomad4 AMR AF: 0.318

Gnomad4 ASJ AF: 0.312

Gnomad4 EAS AF: 0.459

Gnomad4 SAS AF: 0.347

Gnomad4 FIN AF: 0.170

Gnomad4 NFE AF: 0.230

Gnomad4 OTH AF: 0.236

Alfa AF: 0.209 Hom.: 473

Bravo AF: 0.213

Asia WGS AF: 0.349 AC: 1213 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.7
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4237260; hg19: chr9-76741416; COSMIC: COSV60360500;