chr4-148739571-G-A

Position:

• chr4-148739571-G-A

Variant summary

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

The ENST00000661928.1(ENSG00000287292):​n.223-127186G>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 0.136 in 152,156 control chromosomes in the GnomAD database, including 1,752 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 0.14 (1752 hom., cov: 32)
• Consequence: ENST00000661928.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.592

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986195	XR_001741441.2	n.3662-127186G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000661928.1	n.223-127186G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20686 AN: 152038 Hom.: 1754 Cov.: 32

Gnomad AFR AF: 0.0562

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.0624

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.136 AC: 20679 AN: 152156 Hom.: 1752 Cov.: 32 AF XY: 0.133 AC XY: 9889 AN XY: 74386

Gnomad4 AFR AF: 0.0561

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.159

Gnomad4 EAS AF: 0.0624

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.115

Gnomad4 NFE AF: 0.193

Gnomad4 OTH AF: 0.148

Alfa AF: 0.169 Hom.: 475

Bravo AF: 0.133

Asia WGS AF: 0.0920 AC: 321 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.094
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11728154; hg19: chr4-149660723;