7-3089155-T-C

Position:

• chr7-3089155-T-C

Variant summary

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

The ENST00000667422.1(ENSG00000228334):​n.76-1766A>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 0.403 in 152,004 control chromosomes in the GnomAD database, including 13,114 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 0.40 (13114 hom., cov: 32)
• Consequence: ENST00000667422.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.513

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.49 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
	ENST00000667422.1	n.76-1766A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.403 AC: 61236 AN: 151886 Hom.: 13111 Cov.: 32

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.403 AC: 61257 AN: 152004 Hom.: 13114 Cov.: 32 AF XY: 0.405 AC XY: 30066 AN XY: 74276

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.500

Gnomad4 ASJ AF: 0.484

Gnomad4 EAS AF: 0.337

Gnomad4 SAS AF: 0.433

Gnomad4 FIN AF: 0.466

Gnomad4 NFE AF: 0.452

Gnomad4 OTH AF: 0.444

Alfa AF: 0.453 Hom.: 15557

Bravo AF: 0.401

Asia WGS AF: 0.361 AC: 1258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.50
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4722404; hg19: chr7-3128789;