9-103415080-C-T

Variant names:

• chr9-103415080-C-T
• rs6479168
• ENST00000421507.2:n.110+14703G>A

Variant summary

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

The ENST00000421507.2(ENSG00000226566):​n.110+14703G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0781 in 152,186 control chromosomes in the GnomAD database, including 625 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 0.078 (625 hom., cov: 32)
• Consequence: ENSG00000226566 ENST00000421507.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.184
• Publications: 0 publications found

Genes affected

ENSG00000226566 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.156 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
ENSG00000226566	ENST00000421507.2	n.110+14703G>A		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.0780 AC: 11858 AN: 152068 Hom.: 620 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.0253

Gnomad AMR AF: 0.0813

Gnomad ASJ AF: 0.0514

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.0900

Gnomad FIN AF: 0.0295

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0425

Gnomad OTH AF: 0.0722

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

GnomAD4 genome AF: 0.0781 AC: 11892 AN: 152186 Hom.: 625 Cov.: 32 AF XY: 0.0785 AC XY: 5840 AN XY: 74424

African (AFR) AF: 0.139 AC: 5782 AN: 41526

American (AMR) AF: 0.0816 AC: 1247 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0514 AC: 178 AN: 3466

East Asian (EAS) AF: 0.166 AC: 856 AN: 5166

South Asian (SAS) AF: 0.0901 AC: 435 AN: 4830

European-Finnish (FIN) AF: 0.0295 AC: 313 AN: 10612

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0425 AC: 2889 AN: 67990

Other (OTH) AF: 0.0705 AC: 149 AN: 2114

Alfa AF: 0.0537 Hom.: 443

Bravo AF: 0.0833

Asia WGS AF: 0.116 AC: 404 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.9
DANN	Benign	0.49
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs6479168; hg19: chr9-106177362;