rs1611710

Positions:

• chr6-29861139-C-T

Variant summary

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

The ENST00000647952.1(ENSG00000290870):​n.2063-3701G>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 0.451 in 151,906 control chromosomes in the GnomAD database, including 15,584 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 0.45 (15584 hom., cov: 30)
• Consequence: ENST00000647952.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.599

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.551 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
	ENST00000647952.1	n.2063-3701G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68412 AN: 151788 Hom.: 15565 Cov.: 30

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.451 AC: 68459 AN: 151906 Hom.: 15584 Cov.: 30 AF XY: 0.448 AC XY: 33276 AN XY: 74244

Gnomad4 AFR AF: 0.496

Gnomad4 AMR AF: 0.471

Gnomad4 ASJ AF: 0.455

Gnomad4 EAS AF: 0.462

Gnomad4 SAS AF: 0.569

Gnomad4 FIN AF: 0.307

Gnomad4 NFE AF: 0.430

Gnomad4 OTH AF: 0.475

Alfa AF: 0.437 Hom.: 5748

Bravo AF: 0.463

Asia WGS AF: 0.579 AC: 2016 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.4
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: rs1611710; hg19: chr6-29828916;