5-7243868-T-G

Variant names:

• chr5-7243868-T-G
• rs4537030
• ENST00000835169.1:n.123+6771A>C

Variant summary

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

The ENST00000835169.1(ENSG00000308577):​n.123+6771A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 151,800 control chromosomes in the GnomAD database, including 8,153 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 0.32 (8153 hom., cov: 31)
• Consequence: ENSG00000308577 ENST00000835169.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.151
• Publications: 4 publications found

Genes affected

ENSG00000308577 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.398 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000835169.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000308577	ENST00000835169.1		n.123+6771A>C		intron	N/A
	ENSG00000308577	ENST00000835170.1		n.96+6771A>C		intron	N/A
	ENSG00000308577	ENST00000835171.1		n.94+6771A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.316 AC: 47873 AN: 151682 Hom.: 8147 Cov.: 31

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.315 AC: 47886 AN: 151800 Hom.: 8153 Cov.: 31 AF XY: 0.318 AC XY: 23597 AN XY: 74162

African (AFR) AF: 0.192 AC: 7935 AN: 41406

American (AMR) AF: 0.322 AC: 4916 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.375 AC: 1300 AN: 3468

East Asian (EAS) AF: 0.413 AC: 2086 AN: 5052

South Asian (SAS) AF: 0.305 AC: 1466 AN: 4808

European-Finnish (FIN) AF: 0.391 AC: 4120 AN: 10538

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.364 AC: 24709 AN: 67950

Other (OTH) AF: 0.357 AC: 754 AN: 2110

Alfa AF: 0.339 Hom.: 4605

Bravo AF: 0.308

Asia WGS AF: 0.364 AC: 1264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.1
DANN	Benign	0.76
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs4537030; hg19: chr5-7243981;