chr6-32420531-C-T

Variant names:

• chr6-32420531-C-T
• rs2395167
• ENST00000766247.1:n.282+6161C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000766247.1(ENSG00000299769):​n.282+6161C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,120 control chromosomes in the GnomAD database, including 1,511 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 0.13 (1511 hom., cov: 32)
• Consequence: ENSG00000299769 ENST00000766247.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0550
• Publications: 14 publications found

Genes affected

ENSG00000299769 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.168 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
ENSG00000299769	ENST00000766247.1	n.282+6161C>T		intron_variant	Intron 2 of 2
ENSG00000299769	ENST00000766248.1	n.287-4837C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19352 AN: 152002 Hom.: 1511 Cov.: 32

Gnomad AFR AF: 0.0667

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.0893

Gnomad EAS AF: 0.0396

Gnomad SAS AF: 0.0461

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.127 AC: 19358 AN: 152120 Hom.: 1511 Cov.: 32 AF XY: 0.124 AC XY: 9244 AN XY: 74358

African (AFR) AF: 0.0669 AC: 2777 AN: 41520

American (AMR) AF: 0.111 AC: 1701 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0893 AC: 310 AN: 3470

East Asian (EAS) AF: 0.0395 AC: 204 AN: 5168

South Asian (SAS) AF: 0.0455 AC: 220 AN: 4830

European-Finnish (FIN) AF: 0.205 AC: 2164 AN: 10572

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11618 AN: 67960

Other (OTH) AF: 0.120 AC: 254 AN: 2114

Alfa AF: 0.153 Hom.: 3210

Bravo AF: 0.119

Asia WGS AF: 0.0570 AC: 197 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.6
DANN	Benign	0.27
PhyloP100		-0.055

Splicing

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

Other links and lift over

dbSNP: rs2395167; hg19: chr6-32388308;