rs4743556

Variant names:

• chr9-96122663-C-T
• rs4743556
• ENST00000785622.1:n.167+7350G>A

Variant summary

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

The ENST00000785622.1(ENSG00000275465):​n.167+7350G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 152,034 control chromosomes in the GnomAD database, including 4,428 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 0.23 (4428 hom., cov: 33)
• Consequence: ENSG00000275465 ENST00000785622.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.538
• Publications: 3 publications found

Genes affected

ENSG00000275465 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.353 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
ENSG00000275465	ENST00000785622.1	n.167+7350G>A		intron_variant	Intron 2 of 3
ENSG00000287187	ENST00000785720.1	n.120+75C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34601 AN: 151914 Hom.: 4404 Cov.: 33

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.0451

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.228 AC: 34674 AN: 152034 Hom.: 4428 Cov.: 33 AF XY: 0.235 AC XY: 17461 AN XY: 74328

African (AFR) AF: 0.281 AC: 11642 AN: 41442

American (AMR) AF: 0.361 AC: 5520 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 537 AN: 3468

East Asian (EAS) AF: 0.321 AC: 1657 AN: 5164

South Asian (SAS) AF: 0.297 AC: 1434 AN: 4822

European-Finnish (FIN) AF: 0.216 AC: 2279 AN: 10572

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10976 AN: 67968

Other (OTH) AF: 0.240 AC: 506 AN: 2112

Alfa AF: 0.192 Hom.: 10161

Bravo AF: 0.244

Asia WGS AF: 0.355 AC: 1232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.6
DANN	Benign	0.60
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs4743556; hg19: chr9-98884945;