rs1611715

chr6-29861705-A-C

Variant summary

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

The ENST00000647952.1(ENSG00000290870):n.2063-4267T>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 0.298 in 152,146 control chromosomes in the GnomAD database, including 6,925 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 0.30 (6925 hom., cov: 32)
• Consequence: ENST00000647952.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.665

Genes affected

(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 = 0.35 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000647952.1	n.2063-4267T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.298 AC: 45302 AN: 152028 Hom.: 6919 Cov.: 32

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.383

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.298 AC: 45326 AN: 152146 Hom.: 6925 Cov.: 32 AF XY: 0.295 AC XY: 21972 AN XY: 74376

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.306

Gnomad4 ASJ AF: 0.216

Gnomad4 EAS AF: 0.364

Gnomad4 SAS AF: 0.165

Gnomad4 FIN AF: 0.345

Gnomad4 NFE AF: 0.332

Gnomad4 OTH AF: 0.285

Alfa AF: 0.323 Hom.: 2376

Bravo AF: 0.297

Asia WGS AF: 0.214 AC: 746 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	1.2
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1611715; hg19: chr6-29829482;