6-36646035-T-G

Variant names:

• chr6-36646035-T-G
• rs6457931
• ENST00000778909.1:n.192+14646A>C

Variant summary

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

The ENST00000778909.1(ENSG00000301446):​n.192+14646A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.492 in 151,968 control chromosomes in the GnomAD database, including 19,188 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 0.49 (19188 hom., cov: 31)
• Consequence: ENSG00000301446 ENST00000778909.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0830
• Publications: 5 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000778909.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000301446	ENST00000778909.1		n.192+14646A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74775 AN: 151850 Hom.: 19171 Cov.: 31

Gnomad AFR AF: 0.620

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.604

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.492 AC: 74844 AN: 151968 Hom.: 19188 Cov.: 31 AF XY: 0.489 AC XY: 36307 AN XY: 74276

African (AFR) AF: 0.620 AC: 25655 AN: 41410

American (AMR) AF: 0.553 AC: 8432 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.435 AC: 1511 AN: 3472

East Asian (EAS) AF: 0.604 AC: 3124 AN: 5176

South Asian (SAS) AF: 0.450 AC: 2172 AN: 4832

European-Finnish (FIN) AF: 0.337 AC: 3551 AN: 10540

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.425 AC: 28860 AN: 67970

Other (OTH) AF: 0.530 AC: 1121 AN: 2114

Alfa AF: 0.448 Hom.: 20145

Bravo AF: 0.517

Asia WGS AF: 0.532 AC: 1850 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	11
DANN	Benign	0.69
PhyloP100		0.083

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6457931;

hg19: chr6-36613812;