ENST00000637606.1:n.986-83647C>T

Variant names:

• chr9-82696232-C-T
• rs668853
• ENST00000637606.1:n.986-83647C>T

Variant summary

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

The ENST00000637606.1(ENSG00000290551):​n.986-83647C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.549 in 151,868 control chromosomes in the GnomAD database, including 23,571 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 0.55 (23571 hom., cov: 32)
• Consequence: ENSG00000290551 ENST00000637606.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.412

Genes affected

ENSG00000290551 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.702 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107987087	XR_001746782.2	n.248-83647C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290551	ENST00000637606.1	n.986-83647C>T		intron_variant	Intron 9 of 9	5

Frequencies

GnomAD3 genomes AF: 0.550 AC: 83412 AN: 151752 Hom.: 23572 Cov.: 32

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.722

Gnomad SAS AF: 0.674

Gnomad FIN AF: 0.616

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.549 AC: 83438 AN: 151868 Hom.: 23571 Cov.: 32 AF XY: 0.555 AC XY: 41152 AN XY: 74190

Gnomad4 AFR AF: 0.427

Gnomad4 AMR AF: 0.518

Gnomad4 ASJ AF: 0.600

Gnomad4 EAS AF: 0.722

Gnomad4 SAS AF: 0.674

Gnomad4 FIN AF: 0.616

Gnomad4 NFE AF: 0.597

Gnomad4 OTH AF: 0.591

Alfa AF: 0.593 Hom.: 61623

Bravo AF: 0.533

Asia WGS AF: 0.666 AC: 2317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.3
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs668853; hg19: chr9-85311147;