4-148823366-C-T

Variant names:

• chr4-148823366-C-T
• rs471967
• ENST00000661928.1:n.223-43391C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000661928.1(ENSG00000287292):​n.223-43391C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 151,924 control chromosomes in the GnomAD database, including 12,335 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 0.40 (12335 hom., cov: 32)
• Consequence: ENSG00000287292 ENST00000661928.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0510
• Publications: 0 publications found

Genes affected

ENSG00000287292 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.41).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377481	XR_001741437.2	n.105+1318G>A		intron_variant	Intron 2 of 12
LOC107986195	XR_001741441.2	n.3662-43391C>T		intron_variant	Intron 2 of 3
LOC105377481	XR_007058322.1	n.336+1318G>A		intron_variant	Intron 4 of 14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287292	ENST00000661928.1	n.223-43391C>T		intron_variant	Intron 2 of 3
ENSG00000301224	ENST00000777100.1	n.460+7952G>A		intron_variant	Intron 2 of 6
ENSG00000301224	ENST00000777101.1	n.245-2400G>A		intron_variant	Intron 3 of 8
ENSG00000301224	ENST00000777102.1	n.74+1318G>A		intron_variant	Intron 1 of 7

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60372 AN: 151804 Hom.: 12331 Cov.: 32

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.398 AC: 60404 AN: 151924 Hom.: 12335 Cov.: 32 AF XY: 0.392 AC XY: 29065 AN XY: 74218

African (AFR) AF: 0.453 AC: 18778 AN: 41440

American (AMR) AF: 0.421 AC: 6420 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.367 AC: 1270 AN: 3464

East Asian (EAS) AF: 0.344 AC: 1771 AN: 5150

South Asian (SAS) AF: 0.312 AC: 1503 AN: 4810

European-Finnish (FIN) AF: 0.257 AC: 2717 AN: 10552

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.393 AC: 26725 AN: 67950

Other (OTH) AF: 0.425 AC: 895 AN: 2104

Alfa AF: 0.400 Hom.: 38225

Bravo AF: 0.414

Asia WGS AF: 0.303 AC: 1052 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.41
CADD	Benign	9.6
DANN	Benign	0.70
PhyloP100		-0.051

Splicing

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

Other links and lift over

dbSNP: rs471967; hg19: chr4-149744518;