chr6-78488425-T-G

Variant names:

• chr6-78488425-T-G
• rs997649
• ENST00000715178.1:n.794-675A>C

Variant summary

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

The ENST00000715178.1(ENSG00000230309):​n.794-675A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0267 in 152,214 control chromosomes in the GnomAD database, including 93 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 0.027 (93 hom., cov: 32)
• Consequence: ENSG00000230309 ENST00000715178.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06
• Publications: 0 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=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715178.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000230309	ENST00000715178.1		n.794-675A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0267 AC: 4065 AN: 152096 Hom.: 93 Cov.: 32

Gnomad AFR AF: 0.00526

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.0374

Gnomad ASJ AF: 0.0331

Gnomad EAS AF: 0.00289

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.0227

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0317

Gnomad OTH AF: 0.0311

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

GnomAD4 genome AF: 0.0267 AC: 4069 AN: 152214 Hom.: 93 Cov.: 32 AF XY: 0.0290 AC XY: 2160 AN XY: 74452

African (AFR) AF: 0.00525 AC: 218 AN: 41544

American (AMR) AF: 0.0374 AC: 571 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0331 AC: 115 AN: 3470

East Asian (EAS) AF: 0.00309 AC: 16 AN: 5178

South Asian (SAS) AF: 0.127 AC: 612 AN: 4826

European-Finnish (FIN) AF: 0.0227 AC: 241 AN: 10622

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0318 AC: 2159 AN: 67980

Other (OTH) AF: 0.0308 AC: 65 AN: 2112

Alfa AF: 0.0282 Hom.: 10

Bravo AF: 0.0236

Asia WGS AF: 0.0460 AC: 161 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.3
DANN	Benign	0.62
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs997649; hg19: chr6-79198142;