4-69251224-A-T

Variant names:

• chr4-69251224-A-T
• rs11249532
• ENST00000805771.1:n.1191A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000805771.1(ENSG00000304713):​n.1191A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 152,120 control chromosomes in the GnomAD database, including 3,659 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 0.21 (3659 hom., cov: 32)
• Consequence: ENSG00000304713 ENST00000805771.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0930
• Publications: 0 publications found

Genes affected

ENSG00000304713 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304713	ENST00000805771.1	n.1191A>T		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000304713	ENST00000805772.1	n.1433A>T		non_coding_transcript_exon_variant	Exon 5 of 5
ENSG00000304713	ENST00000805773.1	n.1360A>T		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000304713	ENST00000805774.1	n.1416A>T		non_coding_transcript_exon_variant	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31457 AN: 152002 Hom.: 3649 Cov.: 32

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.207 AC: 31502 AN: 152120 Hom.: 3659 Cov.: 32 AF XY: 0.214 AC XY: 15879 AN XY: 74348

African (AFR) AF: 0.306 AC: 12713 AN: 41494

American (AMR) AF: 0.197 AC: 3012 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 569 AN: 3470

East Asian (EAS) AF: 0.125 AC: 646 AN: 5174

South Asian (SAS) AF: 0.257 AC: 1239 AN: 4830

European-Finnish (FIN) AF: 0.280 AC: 2957 AN: 10562

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.143 AC: 9724 AN: 67998

Other (OTH) AF: 0.198 AC: 419 AN: 2114

Alfa AF: 0.178 Hom.: 338

Bravo AF: 0.205

Asia WGS AF: 0.220 AC: 766 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.6
DANN	Benign	0.23
PhyloP100		0.093

Splicing

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

Other links and lift over

dbSNP: rs11249532; hg19: chr4-70116942;