6-36655466-A-T

Variant names:

• chr6-36655466-A-T
• rs4331968
• ENST00000778909.1:n.192+5215T>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+5215T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 152,182 control chromosomes in the GnomAD database, including 7,035 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 0.29 (7035 hom., cov: 33)
• Consequence: ENSG00000301446 ENST00000778909.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.329
• Publications: 9 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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.417 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+5215T>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44282 AN: 152064 Hom.: 7009 Cov.: 33

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.291 AC: 44354 AN: 152182 Hom.: 7035 Cov.: 33 AF XY: 0.287 AC XY: 21341 AN XY: 74412

African (AFR) AF: 0.422 AC: 17521 AN: 41476

American (AMR) AF: 0.238 AC: 3641 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1247 AN: 3470

East Asian (EAS) AF: 0.171 AC: 885 AN: 5190

South Asian (SAS) AF: 0.325 AC: 1565 AN: 4820

European-Finnish (FIN) AF: 0.192 AC: 2038 AN: 10608

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.243 AC: 16549 AN: 68004

Other (OTH) AF: 0.321 AC: 677 AN: 2112

Alfa AF: 0.268 Hom.: 703

Bravo AF: 0.296

Asia WGS AF: 0.295 AC: 1026 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.2
DANN	Benign	0.84
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs4331968; hg19: chr6-36623243;