rs1906252

Variant names:

• chr6-98102413-C-A
• rs1906252
• ENST00000606913.5:n.240+3143C>A

Your query was ambiguous. Multiple possible variants found:

• 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 ENST00000607032.1(ENSG00000271860):​n.410+3143C>A variant causes a intron 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: ENSG00000271860 ENST00000607032.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.292

Genes affected

ENSG00000271860 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000271860	ENST00000606913.5	n.240+3143C>A		intron_variant	Intron 2 of 4	5
ENSG00000271860	ENST00000607032.1	n.410+3143C>A		intron_variant	Intron 4 of 7	3
ENSG00000271860	ENST00000607823.5	n.352+3143C>A		intron_variant	Intron 4 of 6	5

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;