7-128222749-A-G

Position:

• chr7-128222749-A-G

Variant summary

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

The ENST00000690022.1(ENSG00000289434):​n.244-1209T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.761 in 152,140 control chromosomes in the GnomAD database, including 44,746 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 0.76 (44746 hom., cov: 32)
• Consequence: ENSG00000289434 ENST00000690022.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.30

Genes affected

ENSG00000289434 (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 (EAS) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124901744	XR_007060516.1	n.781-1284A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000289434	ENST00000690022.1	n.244-1209T>C		intron_variant
ENSG00000289434	ENST00000692614.2	n.520-1209T>C		intron_variant
ENSG00000292309	ENST00000710955.1	n.836-1284A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.761 AC: 115707 AN: 152022 Hom.: 44713 Cov.: 32

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.890

Gnomad AMR AF: 0.827

Gnomad ASJ AF: 0.796

Gnomad EAS AF: 0.879

Gnomad SAS AF: 0.799

Gnomad FIN AF: 0.825

Gnomad MID AF: 0.713

Gnomad NFE AF: 0.813

Gnomad OTH AF: 0.765

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

GnomAD4 genome AF: 0.761 AC: 115789 AN: 152140 Hom.: 44746 Cov.: 32 AF XY: 0.764 AC XY: 56843 AN XY: 74376

Gnomad4 AFR AF: 0.610

Gnomad4 AMR AF: 0.827

Gnomad4 ASJ AF: 0.796

Gnomad4 EAS AF: 0.879

Gnomad4 SAS AF: 0.800

Gnomad4 FIN AF: 0.825

Gnomad4 NFE AF: 0.813

Gnomad4 OTH AF: 0.767

Alfa AF: 0.803 Hom.: 65112

Bravo AF: 0.755

Asia WGS AF: 0.847 AC: 2940 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	13
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs791595; hg19: chr7-127862802;