rs1906252

Positions:

• chr6-98102413-C-A
• chr6-98102413-C-G
• chr6-98102413-C-T

Variant summary

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

The ENST00000656098.1(ENSG00000271860):​n.1400+3143C>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 0.393 in 151,410 control chromosomes in the GnomAD database, including 12,671 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 0.39 (12671 hom., cov: 30)
• Consequence: ENST00000656098.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.292

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

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.1400+3143C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59519 AN: 151296 Hom.: 12676 Cov.: 30

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.393 AC: 59507 AN: 151410 Hom.: 12671 Cov.: 30 AF XY: 0.391 AC XY: 28884 AN XY: 73962

Gnomad4 AFR AF: 0.231

Gnomad4 AMR AF: 0.351

Gnomad4 ASJ AF: 0.538

Gnomad4 EAS AF: 0.408

Gnomad4 SAS AF: 0.272

Gnomad4 FIN AF: 0.488

Gnomad4 NFE AF: 0.485

Gnomad4 OTH AF: 0.396

Alfa AF: 0.449 Hom.: 7363

Bravo AF: 0.379

Asia WGS AF: 0.271 AC: 945 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1906252; hg19: chr6-98550289;