4-148813816-A-T

Position:

• chr4-148813816-A-T

Variant summary

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

The ENST00000661928.1(ENSG00000287292):​n.223-52941A>T 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 0.155 in 151,874 control chromosomes in the GnomAD database, including 2,833 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 0.16 (2833 hom., cov: 32)
• Consequence: ENST00000661928.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986195	XR_001741441.2	n.3662-52941A>T		intron_variant, non_coding_transcript_variant
LOC105377481	XR_007058322.1	n.516+6476T>A		intron_variant, non_coding_transcript_variant
LOC105377481	XR_001741437.2	n.285+6476T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000661928.1	n.223-52941A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23601 AN: 151756 Hom.: 2833 Cov.: 32

Gnomad AFR AF: 0.0516

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.155 AC: 23603 AN: 151874 Hom.: 2833 Cov.: 32 AF XY: 0.161 AC XY: 11957 AN XY: 74248

Gnomad4 AFR AF: 0.0515

Gnomad4 AMR AF: 0.356

Gnomad4 ASJ AF: 0.172

Gnomad4 EAS AF: 0.493

Gnomad4 SAS AF: 0.176

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.157

Alfa AF: 0.151 Hom.: 275

Bravo AF: 0.176

Asia WGS AF: 0.250 AC: 869 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	14
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1403454; hg19: chr4-149734968;