chr9-38375218-T-C

Variant names:

• chr9-38375218-T-C
• rs987187
• ENST00000422554.2:n.155-111T>C

Variant summary

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

The ENST00000422554.2(ENSG00000223716):​n.155-111T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.715 in 152,188 control chromosomes in the GnomAD database, including 40,182 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 0.71 (40176 hom., cov: 32)
  • Exomes 𝑓: 1.0 (6 hom.)
• Consequence: ENSG00000223716 ENST00000422554.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.472
• Publications: 3 publications found

Genes affected

ENSG00000223716 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000422554.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000223716	ENST00000422554.2	TSL:3	n.155-111T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.715 AC: 108716 AN: 152056 Hom.: 40145 Cov.: 32

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.929

Gnomad AMR AF: 0.807

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.790

Gnomad SAS AF: 0.785

Gnomad FIN AF: 0.841

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.781

Gnomad OTH AF: 0.746

GnomAD4 exome AF: 1.00 AC: 12 AN: 12 Hom.: 6 AF XY: 1.00 AC XY: 8 AN XY: 8

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AF: 1.00 AC: 2 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 4 AN: 4

Other (OTH) AF: 1.00 AC: 2 AN: 2

GnomAD4 genome AF: 0.715 AC: 108799 AN: 152176 Hom.: 40176 Cov.: 32 AF XY: 0.719 AC XY: 53527 AN XY: 74396

African (AFR) AF: 0.508 AC: 21080 AN: 41494

American (AMR) AF: 0.807 AC: 12345 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.814 AC: 2821 AN: 3466

East Asian (EAS) AF: 0.789 AC: 4085 AN: 5176

South Asian (SAS) AF: 0.787 AC: 3795 AN: 4824

European-Finnish (FIN) AF: 0.841 AC: 8917 AN: 10608

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.781 AC: 53105 AN: 67998

Other (OTH) AF: 0.747 AC: 1575 AN: 2108

Alfa AF: 0.766 Hom.: 29164

Bravo AF: 0.704

Asia WGS AF: 0.780 AC: 2712 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.4
DANN	Benign	0.56
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs987187; hg19: chr9-38375215;