4-148748354-T-C

Variant names:

• chr4-148748354-T-C
• rs10032216
• ENST00000661928.1:n.223-118403T>C

Variant summary

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

The ENST00000661928.1(ENSG00000287292):​n.223-118403T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 152,228 control chromosomes in the GnomAD database, including 9,043 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 0.29 (9043 hom., cov: 33)
• Consequence: ENSG00000287292 ENST00000661928.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.65
• Publications: 22 publications found

Genes affected

ENSG00000287292 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986195	XR_001741441.2	n.3662-118403T>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287292	ENST00000661928.1	n.223-118403T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44430 AN: 152110 Hom.: 9030 Cov.: 33

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.0624

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.292 AC: 44485 AN: 152228 Hom.: 9043 Cov.: 33 AF XY: 0.284 AC XY: 21169 AN XY: 74434

African (AFR) AF: 0.576 AC: 23898 AN: 41516

American (AMR) AF: 0.190 AC: 2906 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 705 AN: 3472

East Asian (EAS) AF: 0.0624 AC: 323 AN: 5180

South Asian (SAS) AF: 0.164 AC: 793 AN: 4828

European-Finnish (FIN) AF: 0.112 AC: 1184 AN: 10602

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.204 AC: 13849 AN: 68006

Other (OTH) AF: 0.285 AC: 603 AN: 2114

Alfa AF: 0.244 Hom.: 8793

Bravo AF: 0.312

Asia WGS AF: 0.132 AC: 462 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	15
DANN	Benign	0.70
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs10032216; hg19: chr4-149669506;