rs60745952

Positions:

• chr4-148827842-T-C

Variant summary

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

The ENST00000661928.1(ENSG00000287292):​n.223-38915T>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 0.124 in 152,154 control chromosomes in the GnomAD database, including 1,296 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 0.12 (1296 hom., cov: 32)
• Consequence: ENST00000661928.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.331

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.142 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986195	XR_001741441.2	n.3662-38915T>C		intron_variant, non_coding_transcript_variant
LOC105377481	XR_007058322.1	n.265-3087A>G		intron_variant, non_coding_transcript_variant
LOC105377481	XR_001741437.2	n.34-3087A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000661928.1	n.223-38915T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18844 AN: 152036 Hom.: 1295 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.00540

Gnomad SAS AF: 0.0376

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.124 AC: 18847 AN: 152154 Hom.: 1296 Cov.: 32 AF XY: 0.119 AC XY: 8887 AN XY: 74386

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.177

Gnomad4 EAS AF: 0.00541

Gnomad4 SAS AF: 0.0376

Gnomad4 FIN AF: 0.115

Gnomad4 NFE AF: 0.144

Gnomad4 OTH AF: 0.123

Alfa AF: 0.141 Hom.: 310

Bravo AF: 0.125

Asia WGS AF: 0.0310 AC: 109 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.6
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs60745952; hg19: chr4-149748994;