6-36659706-C-T

Variant names:

• chr6-36659706-C-T
• rs6920453
• ENST00000778909.1:n.192+975G>A

Variant summary

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

The ENST00000778909.1(ENSG00000301446):​n.192+975G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 152,070 control chromosomes in the GnomAD database, including 7,745 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 (7745 hom., cov: 33)
• Consequence: ENSG00000301446 ENST00000778909.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.448
• Publications: 7 publications found

Genes affected

ENSG00000301446 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.442 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
ENSG00000301446	ENST00000778909.1	n.192+975G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45142 AN: 151952 Hom.: 7721 Cov.: 33

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.297 AC: 45227 AN: 152070 Hom.: 7745 Cov.: 33 AF XY: 0.298 AC XY: 22127 AN XY: 74334

African (AFR) AF: 0.447 AC: 18538 AN: 41452

American (AMR) AF: 0.367 AC: 5602 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 454 AN: 3470

East Asian (EAS) AF: 0.434 AC: 2242 AN: 5166

South Asian (SAS) AF: 0.275 AC: 1322 AN: 4814

European-Finnish (FIN) AF: 0.192 AC: 2028 AN: 10568

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.208 AC: 14119 AN: 67996

Other (OTH) AF: 0.274 AC: 580 AN: 2114

Alfa AF: 0.154 Hom.: 382

Bravo AF: 0.321

Asia WGS AF: 0.355 AC: 1236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.8
DANN	Benign	0.56
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs6920453; hg19: chr6-36627483;