6-78557764-T-C

Variant names:

• chr6-78557764-T-C
• rs623155
• ENST00000715178.1:n.332-36442A>G

Variant summary

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

The ENST00000715178.1(ENSG00000230309):​n.332-36442A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 152,062 control chromosomes in the GnomAD database, including 17,956 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 0.48 (17956 hom., cov: 32)
• Consequence: ENSG00000230309 ENST00000715178.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634
• Publications: 3 publications found

Genes affected

ENSG00000230309 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.516 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
ENSG00000230309	ENST00000715178.1	n.332-36442A>G		intron_variant	Intron 2 of 14
ENSG00000230309	ENST00000830453.1	n.120-46507A>G		intron_variant	Intron 2 of 2
ENSG00000230309	ENST00000830454.1	n.161-46507A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73587 AN: 151944 Hom.: 17931 Cov.: 32

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.484 AC: 73668 AN: 152062 Hom.: 17956 Cov.: 32 AF XY: 0.484 AC XY: 35999 AN XY: 74340

African (AFR) AF: 0.522 AC: 21623 AN: 41462

American (AMR) AF: 0.494 AC: 7553 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.458 AC: 1591 AN: 3472

East Asian (EAS) AF: 0.319 AC: 1649 AN: 5172

South Asian (SAS) AF: 0.443 AC: 2138 AN: 4830

European-Finnish (FIN) AF: 0.519 AC: 5474 AN: 10554

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.473 AC: 32166 AN: 67986

Other (OTH) AF: 0.475 AC: 1001 AN: 2108

Alfa AF: 0.482 Hom.: 2870

Bravo AF: 0.482

Asia WGS AF: 0.335 AC: 1166 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.3
DANN	Benign	0.65
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs623155; hg19: chr6-79267481; COSMIC: COSV69406800;