chr7-12890775-C-T

Variant names:

• chr7-12890775-C-T
• rs1019171
• ENST00000638964.1:n.484+88043C>T

Variant summary

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

The ENST00000638964.1(ENSG00000229618):​n.484+88043C>T variant causes a intron 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: ENSG00000229618 ENST00000638964.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.103
• Publications: 2 publications found

Genes affected

ENSG00000229618 (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 (AMR) allele frequency at 95% confidence interval = 0.362 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
ENSG00000229618	ENST00000638964.1	n.484+88043C>T		intron_variant	Intron 1 of 5	5
ENSG00000229618	ENST00000639998.1	n.483+132459C>T		intron_variant	Intron 3 of 7	5
ENSG00000301864	ENST00000782366.1	n.64-1521C>T		intron_variant	Intron 1 of 2

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

African (AFR) AF: 0.218 AC: 9023 AN: 41470

American (AMR) AF: 0.370 AC: 5656 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.349 AC: 1209 AN: 3466

East Asian (EAS) AF: 0.308 AC: 1594 AN: 5168

South Asian (SAS) AF: 0.361 AC: 1739 AN: 4816

European-Finnish (FIN) AF: 0.270 AC: 2845 AN: 10546

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.349 AC: 23746 AN: 67944

Other (OTH) AF: 0.325 AC: 685 AN: 2110

Alfa AF: 0.319 Hom.: 4050

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
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs1019171; hg19: chr7-12930400;