4-148725386-T-C

Position:

• chr4-148725386-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000661928.1(ENSG00000287292):​n.223-141371T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 152,102 control chromosomes in the GnomAD database, including 4,850 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 (4850 hom., cov: 32)
• Consequence: ENST00000661928.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0990

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986195	XR_001741441.2	n.3662-141371T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000661928.1	n.223-141371T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35360 AN: 151984 Hom.: 4849 Cov.: 32

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.0633

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.226

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.233 AC: 35382 AN: 152102 Hom.: 4850 Cov.: 32 AF XY: 0.226 AC XY: 16777 AN XY: 74396

Gnomad4 AFR AF: 0.384

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.0633

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.115

Gnomad4 NFE AF: 0.196

Gnomad4 OTH AF: 0.230

Alfa AF: 0.138 Hom.: 328

Bravo AF: 0.246

Asia WGS AF: 0.113 AC: 396 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.3
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs28435578; hg19: chr4-149646538;