rs939207

chr4-68301953-C-T

Variant summary

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

The ENST00000509466.2(ENSG00000249531):n.734-372C>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 0.0986 in 152,012 control chromosomes in the GnomAD database, including 1,140 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 0.099 (1140 hom., cov: 32)
• Consequence: ENST00000509466.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000509466.2	n.734-372C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0987 AC: 14985 AN: 151894 Hom.: 1139 Cov.: 32

Gnomad AFR AF: 0.0245

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.0697

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.0287

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.0822

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

GnomAD4 genome AF: 0.0986 AC: 14989 AN: 152012 Hom.: 1140 Cov.: 32 AF XY: 0.103 AC XY: 7682 AN XY: 74288

Gnomad4 AFR AF: 0.0244

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.0697

Gnomad4 EAS AF: 0.372

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.111

Gnomad4 OTH AF: 0.0833

Alfa AF: 0.102 Hom.: 1094

Bravo AF: 0.0919

Asia WGS AF: 0.238 AC: 818 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.22
Dann	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs939207; hg19: chr4-69167671;