rs1723623

Variant names:

• chr7-110138270-G-A
• rs1723623
• ENST00000658032.1:n.439-27569C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-110138270-G-A
• chr7-110138270-G-T

Variant summary

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

The ENST00000658032.1(ENSG00000226965):​n.439-27569C>T variant causes a intron 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: ENSG00000226965 ENST00000658032.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.517
• Publications: 1 publications found

Genes affected

ENSG00000226965 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000658032.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000226965	ENST00000658032.1		n.439-27569C>T		intron	N/A
	ENSG00000226965	ENST00000667232.1		n.520-27569C>T		intron	N/A
	ENSG00000226965	ENST00000755897.1		n.34-29940C>T		intron	N/A

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

African (AFR) AF: 0.405 AC: 16723 AN: 41304

American (AMR) AF: 0.506 AC: 7693 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1187 AN: 3464

East Asian (EAS) AF: 0.321 AC: 1643 AN: 5120

South Asian (SAS) AF: 0.457 AC: 2194 AN: 4804

European-Finnish (FIN) AF: 0.542 AC: 5704 AN: 10526

Middle Eastern (MID) AF: 0.356 AC: 104 AN: 292

European-Non Finnish (NFE) AF: 0.575 AC: 38967 AN: 67812

Other (OTH) AF: 0.480 AC: 1008 AN: 2098

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.73
DANN	Benign	0.50
PhyloP100		0.52

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1723623;

hg19: chr7-109778327;