6-7431526-C-T

Variant names:

• chr6-7431526-C-T
• rs9379104
• ENST00000797726.1:n.65+4595C>T

Variant summary

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

The ENST00000797726.1(ENSG00000303868):​n.65+4595C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,230 control chromosomes in the GnomAD database, including 1,174 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 0.10 (1174 hom., cov: 32)
• Consequence: ENSG00000303868 ENST00000797726.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 2 publications found

Genes affected

ENSG00000303868 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724234	XR_427872.3	n.151+1389C>T		intron_variant	Intron 2 of 2
LOC102724234	XR_926434.2	n.151+1389C>T		intron_variant	Intron 2 of 2
LOC102724234	XR_926435.2	n.151+1389C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303868	ENST00000797726.1	n.65+4595C>T		intron_variant	Intron 1 of 4
ENSG00000303868	ENST00000797727.1	n.64+4595C>T		intron_variant	Intron 1 of 2
ENSG00000303868	ENST00000797728.1	n.63+4595C>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15729 AN: 152112 Hom.: 1174 Cov.: 32

Gnomad AFR AF: 0.0391

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0958

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.103 AC: 15727 AN: 152230 Hom.: 1174 Cov.: 32 AF XY: 0.110 AC XY: 8165 AN XY: 74414

African (AFR) AF: 0.0390 AC: 1622 AN: 41552

American (AMR) AF: 0.210 AC: 3211 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 396 AN: 3468

East Asian (EAS) AF: 0.317 AC: 1638 AN: 5162

South Asian (SAS) AF: 0.135 AC: 650 AN: 4828

European-Finnish (FIN) AF: 0.122 AC: 1290 AN: 10600

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0957 AC: 6511 AN: 68006

Other (OTH) AF: 0.112 AC: 237 AN: 2112

Alfa AF: 0.0975 Hom.: 411

Bravo AF: 0.106

Asia WGS AF: 0.200 AC: 694 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.24
DANN	Benign	0.80
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs9379104; hg19: chr6-7431759;