rs1723623

chr7-110138270-G-Achr7-110138270-G-T

Variant summary

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

The ENST00000667232.1(ENSG00000226965):n.520-27569C>T 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 0.499 in 151,530 control chromosomes in the GnomAD database, including 19,373 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 0.50 (19373 hom., cov: 30)
• Consequence: ENST00000667232.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.517

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.57 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
	ENST00000667232.1	n.520-27569C>T		intron_variant, non_coding_transcript_variant
	ENST00000658032.1	n.439-27569C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.499 AC: 75546 AN: 151412 Hom.: 19364 Cov.: 30

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.379

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.485

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

GnomAD4 genome AF: 0.499 AC: 75582 AN: 151530 Hom.: 19373 Cov.: 30 AF XY: 0.496 AC XY: 36741 AN XY: 74022

Gnomad4 AFR AF: 0.405

Gnomad4 AMR AF: 0.506

Gnomad4 ASJ AF: 0.343

Gnomad4 EAS AF: 0.321

Gnomad4 SAS AF: 0.457

Gnomad4 FIN AF: 0.542

Gnomad4 NFE AF: 0.575

Gnomad4 OTH AF: 0.480

Alfa AF: 0.535 Hom.: 2768

Bravo AF: 0.490

Asia WGS AF: 0.356 AC: 1236 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.73
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1723623; hg19: chr7-109778327;