rs1611635

Variant names:

• chr6-29868686-C-T
• rs1611635
• ENST00000647952.1:n.2063-11248G>A

Variant summary

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

The ENST00000647952.1(ENSG00000290870):​n.2063-11248G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 152,278 control chromosomes in the GnomAD database, including 1,108 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 0.10 (1108 hom., cov: 33)
• Consequence: ENSG00000290870 ENST00000647952.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

Genes affected

ENSG00000290870 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.159 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
ENSG00000290870	ENST00000647952.1	n.2063-11248G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15789 AN: 152160 Hom.: 1108 Cov.: 33

Gnomad AFR AF: 0.0334

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.0675

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.0183

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.0781

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.0981

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

GnomAD4 genome AF: 0.104 AC: 15782 AN: 152278 Hom.: 1108 Cov.: 33 AF XY: 0.0988 AC XY: 7354 AN XY: 74460

Gnomad4 AFR AF: 0.0333

Gnomad4 AMR AF: 0.0674

Gnomad4 ASJ AF: 0.121

Gnomad4 EAS AF: 0.0183

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.0781

Gnomad4 NFE AF: 0.162

Gnomad4 OTH AF: 0.0975

Alfa AF: 0.148 Hom.: 2337

Bravo AF: 0.0984

Asia WGS AF: 0.0630 AC: 222 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1611635; hg19: chr6-29836463;