7-128204042-A-G

Position:

• chr7-128204042-A-G

Variant summary

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

The ENST00000710955.1(ENSG00000292309):​n.306-1647A>G 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 0.882 in 152,148 control chromosomes in the GnomAD database, including 59,358 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 0.88 (59358 hom., cov: 31)
• Consequence: ENST00000710955.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.911 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000710955.1	n.306-1647A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.882 AC: 134044 AN: 152030 Hom.: 59318 Cov.: 31

Gnomad AFR AF: 0.848

Gnomad AMI AF: 0.959

Gnomad AMR AF: 0.797

Gnomad ASJ AF: 0.868

Gnomad EAS AF: 0.908

Gnomad SAS AF: 0.808

Gnomad FIN AF: 0.930

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.917

Gnomad OTH AF: 0.878

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

GnomAD4 genome AF: 0.882 AC: 134138 AN: 152148 Hom.: 59358 Cov.: 31 AF XY: 0.878 AC XY: 65310 AN XY: 74366

Gnomad4 AFR AF: 0.849

Gnomad4 AMR AF: 0.796

Gnomad4 ASJ AF: 0.868

Gnomad4 EAS AF: 0.908

Gnomad4 SAS AF: 0.809

Gnomad4 FIN AF: 0.930

Gnomad4 NFE AF: 0.917

Gnomad4 OTH AF: 0.879

Alfa AF: 0.893 Hom.: 37596

Bravo AF: 0.869

Asia WGS AF: 0.854 AC: 2969 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.84
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4731416; hg19: chr7-127844095;