rs12529874

Positions:

• chr6-98014625-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BS1 BS2

The ENST00000656098.1(ENSG00000271860):​n.1315+45159G>A variant causes a intron, non coding transcript change. The variant allele was found at a frequency of 0.027 in 152,014 control chromosomes in the GnomAD database, including 74 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 0.027 (74 hom., cov: 32)
• Consequence: ENST00000656098.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.04

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.41).
• BS1: Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.027 (4099/152014) while in subpopulation EAS AF= 0.0454 (233/5128). AF 95% confidence interval is 0.0407. There are 74 homozygotes in gnomad4. There are 2051 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 74 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000656098.1	n.1315+45159G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0269 AC: 4092 AN: 151896 Hom.: 75 Cov.: 32

Gnomad AFR AF: 0.00740

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.0290

Gnomad ASJ AF: 0.0631

Gnomad EAS AF: 0.0459

Gnomad SAS AF: 0.0344

Gnomad FIN AF: 0.0296

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0330

Gnomad OTH AF: 0.0388

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

GnomAD4 genome AF: 0.0270 AC: 4099 AN: 152014 Hom.: 74 Cov.: 32 AF XY: 0.0276 AC XY: 2051 AN XY: 74314

Gnomad4 AFR AF: 0.00737

Gnomad4 AMR AF: 0.0289

Gnomad4 ASJ AF: 0.0631

Gnomad4 EAS AF: 0.0454

Gnomad4 SAS AF: 0.0352

Gnomad4 FIN AF: 0.0296

Gnomad4 NFE AF: 0.0330

Gnomad4 OTH AF: 0.0413

Alfa AF: 0.0309 Hom.: 31

Bravo AF: 0.0251

Asia WGS AF: 0.0700 AC: 243 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.41
CADD	Benign	19
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12529874; hg19: chr6-98462501;