7-12890775-C-T

Position:

• chr7-12890775-C-T

Variant summary

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

The ENST00000639998.1(ENSG00000229618):​n.483+132459C>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 0.309 in 151,998 control chromosomes in the GnomAD database, including 7,511 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 0.31 (7511 hom., cov: 32)
• Consequence: ENST00000639998.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.103

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.362 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000639998.1	n.483+132459C>T		intron_variant, non_coding_transcript_variant		5
	ENST00000638964.1	n.484+88043C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46931 AN: 151880 Hom.: 7506 Cov.: 32

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.309 AC: 46952 AN: 151998 Hom.: 7511 Cov.: 32 AF XY: 0.306 AC XY: 22751 AN XY: 74274

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.370

Gnomad4 ASJ AF: 0.349

Gnomad4 EAS AF: 0.308

Gnomad4 SAS AF: 0.361

Gnomad4 FIN AF: 0.270

Gnomad4 NFE AF: 0.349

Gnomad4 OTH AF: 0.325

Alfa AF: 0.316 Hom.: 3604

Bravo AF: 0.312

Asia WGS AF: 0.296 AC: 1032 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.2
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1019171; hg19: chr7-12930400;