rs2778624

Variant names:

• chr9-122446782-T-C
• rs2778624
• ENST00000431442.3:n.324-647T>C

Variant summary

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

The ENST00000431442.3(ENSG00000234156):​n.324-647T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.666 in 151,994 control chromosomes in the GnomAD database, including 34,420 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 0.67 (34420 hom., cov: 31)
• Consequence: ENSG00000234156 ENST00000431442.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.167
• Publications: 5 publications found

Genes affected

ENSG00000234156 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.731 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
ENSG00000234156	ENST00000431442.3	n.324-647T>C		intron_variant	Intron 3 of 9	3
ENSG00000234156	ENST00000433572.3	n.358-647T>C		intron_variant	Intron 4 of 6	3
ENSG00000234156	ENST00000723589.1	n.420-21779T>C		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.666 AC: 101109 AN: 151876 Hom.: 34404 Cov.: 31

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.637

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.624

Gnomad FIN AF: 0.790

Gnomad MID AF: 0.624

Gnomad NFE AF: 0.736

Gnomad OTH AF: 0.660

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

GnomAD4 genome AF: 0.666 AC: 101163 AN: 151994 Hom.: 34420 Cov.: 31 AF XY: 0.666 AC XY: 49505 AN XY: 74302

African (AFR) AF: 0.523 AC: 21674 AN: 41430

American (AMR) AF: 0.661 AC: 10094 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.637 AC: 2211 AN: 3470

East Asian (EAS) AF: 0.692 AC: 3572 AN: 5160

South Asian (SAS) AF: 0.625 AC: 3002 AN: 4806

European-Finnish (FIN) AF: 0.790 AC: 8349 AN: 10574

Middle Eastern (MID) AF: 0.613 AC: 179 AN: 292

European-Non Finnish (NFE) AF: 0.736 AC: 50048 AN: 67984

Other (OTH) AF: 0.659 AC: 1383 AN: 2100

Alfa AF: 0.712 Hom.: 157039

Bravo AF: 0.653

Asia WGS AF: 0.624 AC: 2169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	6.4
DANN	Benign	0.76
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs2778624; hg19: chr9-125209061;