rs6973392

Variant names:

• chr7-89431419-C-T
• rs6973392
• ENST00000818316.1:n.95-38184C>T

Variant summary

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

The ENST00000818316.1(ENSG00000227863):​n.95-38184C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 152,088 control chromosomes in the GnomAD database, including 3,270 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 0.16 (3270 hom., cov: 32)
• Consequence: ENSG00000227863 ENST00000818316.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200
• Publications: 1 publications found

Genes affected

ENSG00000227863 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.352 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
ENSG00000227863	ENST00000818316.1	n.95-38184C>T		intron_variant	Intron 1 of 2
ENSG00000227863	ENST00000818318.1	n.95-38184C>T		intron_variant	Intron 1 of 2
ENSG00000227863	ENST00000818319.1	n.94-38184C>T		intron_variant	Intron 1 of 2
ENSG00000227863	ENST00000818320.1	n.80+12938C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24817 AN: 151970 Hom.: 3254 Cov.: 32

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.0354

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.0781

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.164 AC: 24882 AN: 152088 Hom.: 3270 Cov.: 32 AF XY: 0.160 AC XY: 11896 AN XY: 74366

African (AFR) AF: 0.357 AC: 14790 AN: 41440

American (AMR) AF: 0.118 AC: 1806 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 816 AN: 3472

East Asian (EAS) AF: 0.105 AC: 542 AN: 5172

South Asian (SAS) AF: 0.150 AC: 724 AN: 4822

European-Finnish (FIN) AF: 0.0354 AC: 375 AN: 10600

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.0781 AC: 5309 AN: 67998

Other (OTH) AF: 0.185 AC: 390 AN: 2108

Alfa AF: 0.119 Hom.: 2870

Bravo AF: 0.181

Asia WGS AF: 0.168 AC: 583 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.47
PhyloP100		-0.0020

Splicing

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

Other links and lift over

dbSNP: rs6973392; hg19: chr7-89060733;