chr6-78813209-T-G

Variant names:

• chr6-78813209-T-G
• rs9361448
• ENST00000430931.1:n.95A>C

Variant summary

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

The ENST00000430931.1(ENSG00000229495):​n.95A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.758 in 145,004 control chromosomes in the GnomAD database, including 44,758 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 0.76 (44758 hom., cov: 28)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000229495 ENST00000430931.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.139
• Publications: 6 publications found

Genes affected

ENSG00000229495 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000430931.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000229495	ENST00000430931.1	TSL:5	n.95A>C		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.758 AC: 109756 AN: 144882 Hom.: 44725 Cov.: 28

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.763

Gnomad AMR AF: 0.820

Gnomad ASJ AF: 0.723

Gnomad EAS AF: 0.862

Gnomad SAS AF: 0.870

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.713

Gnomad NFE AF: 0.760

Gnomad OTH AF: 0.757

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.758 AC: 109843 AN: 145004 Hom.: 44758 Cov.: 28 AF XY: 0.762 AC XY: 53684 AN XY: 70430

African (AFR) AF: 0.704 AC: 27777 AN: 39476

American (AMR) AF: 0.820 AC: 12053 AN: 14698

Ashkenazi Jewish (ASJ) AF: 0.723 AC: 2452 AN: 3392

East Asian (EAS) AF: 0.862 AC: 4207 AN: 4878

South Asian (SAS) AF: 0.871 AC: 4001 AN: 4596

European-Finnish (FIN) AF: 0.772 AC: 7307 AN: 9468

Middle Eastern (MID) AF: 0.699 AC: 200 AN: 286

European-Non Finnish (NFE) AF: 0.760 AC: 49656 AN: 65332

Other (OTH) AF: 0.760 AC: 1505 AN: 1980

Alfa AF: 0.763 Hom.: 36528

Asia WGS AF: 0.854 AC: 2915 AN: 3414

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.4
DANN	Benign	0.71
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs9361448; hg19: chr6-79522926;