chr19-43692516-T-C

Variant names:

• chr19-43692516-T-C
• rs740587
• ENST00000636801.1:n.298+97T>C

Variant summary

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

The ENST00000636801.1(ENSG00000283525):​n.298+97T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.468 in 151,872 control chromosomes in the GnomAD database, including 16,811 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 0.47 (16809 hom., cov: 31)
  • Exomes 𝑓: 0.43 (2 hom.)
• Consequence: ENSG00000283525 ENST00000636801.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.146
• Publications: 1 publications found

Genes affected

ENSG00000283525 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.53 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372412	NR_172891.1	n.964+97T>C		intron_variant	Intron 3 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000283525	ENST00000636801.1	n.298+97T>C		intron_variant	Intron 2 of 5	6
ENSG00000290609	ENST00000637093.1	n.138+97T>C		intron_variant	Intron 1 of 4	5

Frequencies

GnomAD3 genomes AF: 0.468 AC: 71047 AN: 151724 Hom.: 16795 Cov.: 31

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.486

GnomAD4 exome AF: 0.429 AC: 12 AN: 28 Hom.: 2 AF XY: 0.438 AC XY: 7 AN XY: 16

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.550 AC: 11 AN: 20

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.250 AC: 1 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.468 AC: 71099 AN: 151844 Hom.: 16809 Cov.: 31 AF XY: 0.467 AC XY: 34667 AN XY: 74198

African (AFR) AF: 0.499 AC: 20653 AN: 41360

American (AMR) AF: 0.540 AC: 8232 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.559 AC: 1941 AN: 3470

East Asian (EAS) AF: 0.532 AC: 2746 AN: 5162

South Asian (SAS) AF: 0.465 AC: 2239 AN: 4816

European-Finnish (FIN) AF: 0.371 AC: 3904 AN: 10526

Middle Eastern (MID) AF: 0.521 AC: 152 AN: 292

European-Non Finnish (NFE) AF: 0.438 AC: 29740 AN: 67950

Other (OTH) AF: 0.485 AC: 1025 AN: 2114

Alfa AF: 0.467 Hom.: 11559

Bravo AF: 0.489

Asia WGS AF: 0.513 AC: 1781 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.2
DANN	Benign	0.33
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs740587; hg19: chr19-44196668;