chr6-378970-G-A

Variant names:

• chr6-378970-G-A
• rs9501958
• ENST00000793853.1:n.394+8011C>T

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000793853.1(ENSG00000303358):​n.394+8011C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0927 in 148,122 control chromosomes in the GnomAD database, including 27 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 0.093 (27 hom., cov: 59)
• Consequence: ENSG00000303358 ENST00000793853.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.105
• Publications: 8 publications found

Genes affected

ENSG00000303358 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BS2: High Homozygotes in GnomAd4 at 27 gene

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
ENSG00000303358	ENST00000793853.1	n.394+8011C>T		intron_variant	Intron 1 of 1
ENSG00000303358	ENST00000793854.1	n.264-1050C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0925 AC: 13696 AN: 148022 Hom.: 27 Cov.: 59

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.0770

Gnomad ASJ AF: 0.0589

Gnomad EAS AF: 0.0198

Gnomad SAS AF: 0.0403

Gnomad FIN AF: 0.0380

Gnomad MID AF: 0.119

Gnomad NFE AF: 0.0543

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.0927 AC: 13729 AN: 148122 Hom.: 27 Cov.: 59 AF XY: 0.0910 AC XY: 6591 AN XY: 72454

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.196 AC: 7662 AN: 39144

American (AMR) AF: 0.0768 AC: 1150 AN: 14966

Ashkenazi Jewish (ASJ) AF: 0.0589 AC: 202 AN: 3430

East Asian (EAS) AF: 0.0199 AC: 103 AN: 5178

South Asian (SAS) AF: 0.0401 AC: 191 AN: 4766

European-Finnish (FIN) AF: 0.0380 AC: 399 AN: 10504

Middle Eastern (MID) AF: 0.124 AC: 36 AN: 290

European-Non Finnish (NFE) AF: 0.0543 AC: 3635 AN: 66934

Other (OTH) AF: 0.102 AC: 210 AN: 2050

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.0774 Hom.: 67

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.5
DANN	Benign	0.57
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs9501958; hg19: chr6-378970;