chr6-103997492-C-T

Variant names:

• chr6-103997492-C-T
• rs9499708
• ENST00000843032.1:n.51-11472G>A

Variant summary

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

The ENST00000843032.1(ENSG00000309686):​n.51-11472G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.716 in 151,774 control chromosomes in the GnomAD database, including 40,292 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 0.72 (40292 hom., cov: 31)
• Consequence: ENSG00000309686 ENST00000843032.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.379
• Publications: 7 publications found

Genes affected

ENSG00000309686 (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 (AFR) allele frequency at 95% confidence interval = 0.915 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
ENSG00000309686	ENST00000843032.1	n.51-11472G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.716 AC: 108523 AN: 151656 Hom.: 40230 Cov.: 31

Gnomad AFR AF: 0.923

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.705

Gnomad ASJ AF: 0.630

Gnomad EAS AF: 0.691

Gnomad SAS AF: 0.579

Gnomad FIN AF: 0.740

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.689

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

GnomAD4 genome AF: 0.716 AC: 108647 AN: 151774 Hom.: 40292 Cov.: 31 AF XY: 0.718 AC XY: 53250 AN XY: 74170

African (AFR) AF: 0.923 AC: 38295 AN: 41500

American (AMR) AF: 0.706 AC: 10717 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.630 AC: 2183 AN: 3464

East Asian (EAS) AF: 0.691 AC: 3534 AN: 5112

South Asian (SAS) AF: 0.579 AC: 2790 AN: 4820

European-Finnish (FIN) AF: 0.740 AC: 7817 AN: 10570

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.608 AC: 41213 AN: 67800

Other (OTH) AF: 0.684 AC: 1445 AN: 2112

Alfa AF: 0.642 Hom.: 102324

Bravo AF: 0.725

Asia WGS AF: 0.616 AC: 2143 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.14
DANN	Benign	0.61
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs9499708; hg19: chr6-104445367;