4-148918760-C-A

Position:

• chr4-148918760-C-A

Variant summary

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

The ENST00000661928.1(ENSG00000287292):​n.347+51879C>A 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 0.346 in 151,876 control chromosomes in the GnomAD database, including 10,090 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 0.35 (10090 hom., cov: 32)
• Consequence: ENST00000661928.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.14

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986195	XR_001741441.2	n.3786+51879C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000661928.1	n.347+51879C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52541 AN: 151758 Hom.: 10078 Cov.: 32

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.346 AC: 52601 AN: 151876 Hom.: 10090 Cov.: 32 AF XY: 0.342 AC XY: 25405 AN XY: 74248

Gnomad4 AFR AF: 0.520

Gnomad4 AMR AF: 0.366

Gnomad4 ASJ AF: 0.325

Gnomad4 EAS AF: 0.372

Gnomad4 SAS AF: 0.259

Gnomad4 FIN AF: 0.176

Gnomad4 NFE AF: 0.271

Gnomad4 OTH AF: 0.326

Alfa AF: 0.287 Hom.: 3112

Bravo AF: 0.370

Asia WGS AF: 0.318 AC: 1106 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.022
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4835147; hg19: chr4-149839912;