9-104936331-C-T

Variant names:

• chr9-104936331-C-T
• rs3887137
• ENST00000820514.1:n.1165-2421C>T

Variant summary

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

The ENST00000820514.1(ENSG00000226334):​n.1165-2421C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0975 in 152,078 control chromosomes in the GnomAD database, including 986 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 0.098 (986 hom., cov: 32)
• Consequence: ENSG00000226334 ENST00000820514.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.354
• Publications: 15 publications found

Genes affected

ENSG00000226334 (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 (EAS) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376196	NR_188620.1	n.1340-2421C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000226334	ENST00000820514.1	n.1165-2421C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0976 AC: 14826 AN: 151960 Hom.: 984 Cov.: 32

Gnomad AFR AF: 0.0464

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.0988

Gnomad FIN AF: 0.0982

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.0975 AC: 14829 AN: 152078 Hom.: 986 Cov.: 32 AF XY: 0.0986 AC XY: 7327 AN XY: 74340

African (AFR) AF: 0.0463 AC: 1922 AN: 41486

American (AMR) AF: 0.104 AC: 1594 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 415 AN: 3470

East Asian (EAS) AF: 0.330 AC: 1701 AN: 5160

South Asian (SAS) AF: 0.0991 AC: 478 AN: 4822

European-Finnish (FIN) AF: 0.0982 AC: 1037 AN: 10564

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.109 AC: 7397 AN: 67984

Other (OTH) AF: 0.113 AC: 238 AN: 2112

Alfa AF: 0.101 Hom.: 1544

Bravo AF: 0.0989

Asia WGS AF: 0.190 AC: 663 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.59
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs3887137; hg19: chr9-107698612;