ENST00000499292.2:n.361-5557A>C

Variant names:

• chr4-36267390-A-C
• rs10517377
• ENST00000499292.2:n.361-5557A>C

Variant summary

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

The ENST00000499292.2(ENSG00000247193):​n.361-5557A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 152,214 control chromosomes in the GnomAD database, including 2,993 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 0.18 (2993 hom., cov: 32)
• Consequence: ENSG00000247193 ENST00000499292.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.33
• Publications: 2 publications found

Genes affected

ENSG00000247193 (HGNC:58751):

LOC439933 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC439933	NR_122079.1	n.361-5557A>C		intron_variant	Intron 3 of 4
LOC439933	NR_122080.1	n.338-5845A>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000247193	ENST00000499292.2	n.361-5557A>C		intron_variant	Intron 3 of 4	1
ENSG00000247193	ENST00000502245.3	n.387-5845A>C		intron_variant	Intron 2 of 2	1
ENSG00000247193	ENST00000691596.2	n.229-5845A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27428 AN: 152096 Hom.: 2992 Cov.: 32

Gnomad AFR AF: 0.0674

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.0758

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.180 AC: 27428 AN: 152214 Hom.: 2993 Cov.: 32 AF XY: 0.178 AC XY: 13241 AN XY: 74404

African (AFR) AF: 0.0673 AC: 2795 AN: 41560

American (AMR) AF: 0.223 AC: 3406 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1129 AN: 3470

East Asian (EAS) AF: 0.0762 AC: 395 AN: 5186

South Asian (SAS) AF: 0.236 AC: 1140 AN: 4826

European-Finnish (FIN) AF: 0.153 AC: 1620 AN: 10588

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.237 AC: 16133 AN: 67988

Other (OTH) AF: 0.191 AC: 402 AN: 2104

Alfa AF: 0.128 Hom.: 293

Bravo AF: 0.176

Asia WGS AF: 0.141 AC: 495 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.28
DANN	Benign	0.56
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs10517377; hg19: chr4-36269012;