chr7-121801926-T-A

Variant names:

• chr7-121801926-T-A
• rs10488055
• ENST00000719872.1:n.103+30476A>T

Variant summary

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

The ENST00000719872.1(ENSG00000227743):​n.103+30476A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 151,964 control chromosomes in the GnomAD database, including 7,904 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 0.32 (7904 hom., cov: 31)
• Consequence: ENSG00000227743 ENST00000719872.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.411
• Publications: 4 publications found

Genes affected

ENSG00000227743 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.371 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
ENSG00000227743	ENST00000719872.1	n.103+30476A>T		intron_variant	Intron 1 of 4
ENSG00000227743	ENST00000719873.1	n.139+30476A>T		intron_variant	Intron 1 of 2
ENSG00000227743	ENST00000719874.1	n.113+30476A>T		intron_variant	Intron 1 of 5
ENSG00000227743	ENST00000719875.1	n.102+30476A>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48380 AN: 151846 Hom.: 7896 Cov.: 31

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.319 AC: 48442 AN: 151964 Hom.: 7904 Cov.: 31 AF XY: 0.323 AC XY: 24001 AN XY: 74282

African (AFR) AF: 0.291 AC: 12054 AN: 41476

American (AMR) AF: 0.264 AC: 4036 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.291 AC: 1012 AN: 3472

East Asian (EAS) AF: 0.317 AC: 1635 AN: 5156

South Asian (SAS) AF: 0.386 AC: 1860 AN: 4818

European-Finnish (FIN) AF: 0.372 AC: 3916 AN: 10532

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.340 AC: 23066 AN: 67932

Other (OTH) AF: 0.278 AC: 585 AN: 2108

Alfa AF: 0.337 Hom.: 1123

Bravo AF: 0.301

Asia WGS AF: 0.347 AC: 1207 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.6
DANN	Benign	0.69
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs10488055; hg19: chr7-121441980;