chr6-78235177-G-A

Variant names:

• chr6-78235177-G-A
• rs946138
• ENST00000715178.1:n.1038-31224C>T

Variant summary

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

The ENST00000715178.1(ENSG00000230309):​n.1038-31224C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 152,152 control chromosomes in the GnomAD database, including 1,024 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 0.11 (1024 hom., cov: 32)
• Consequence: ENSG00000230309 ENST00000715178.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.100
• Publications: 4 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.141 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

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
	ENSG00000230309	ENST00000715178.1		n.1038-31224C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17255 AN: 152034 Hom.: 1024 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.0876

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.0626

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.113 AC: 17243 AN: 152152 Hom.: 1024 Cov.: 32 AF XY: 0.111 AC XY: 8231 AN XY: 74370

African (AFR) AF: 0.112 AC: 4653 AN: 41536

American (AMR) AF: 0.0875 AC: 1337 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 696 AN: 3470

East Asian (EAS) AF: 0.149 AC: 771 AN: 5158

South Asian (SAS) AF: 0.105 AC: 507 AN: 4822

European-Finnish (FIN) AF: 0.0626 AC: 663 AN: 10584

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.121 AC: 8216 AN: 67980

Other (OTH) AF: 0.115 AC: 244 AN: 2114

Alfa AF: 0.116 Hom.: 215

Bravo AF: 0.115

Asia WGS AF: 0.146 AC: 506 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.8
DANN	Benign	0.38
PhyloP100		0.10

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: rs946138;

hg19: chr6-78944894;