chr6-43755598-A-C

Variant names:

• chr6-43755598-A-C
• rs833052
• ENST00000770040.1:n.95+2945T>G

Variant summary

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

The ENST00000770040.1(ENSG00000236961):​n.95+2945T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.88 in 152,228 control chromosomes in the GnomAD database, including 59,177 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 (59177 hom., cov: 31)
• Consequence: ENSG00000236961 ENST00000770040.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59
• Publications: 28 publications found

Genes affected

ENSG00000236961 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.942 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000770040.1. 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
	ENSG00000236961	ENST00000770040.1		n.95+2945T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.880 AC: 133808 AN: 152110 Hom.: 59113 Cov.: 31

Gnomad AFR AF: 0.950

Gnomad AMI AF: 0.819

Gnomad AMR AF: 0.855

Gnomad ASJ AF: 0.895

Gnomad EAS AF: 0.682

Gnomad SAS AF: 0.842

Gnomad FIN AF: 0.843

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.866

Gnomad OTH AF: 0.882

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

GnomAD4 genome AF: 0.880 AC: 133925 AN: 152228 Hom.: 59177 Cov.: 31 AF XY: 0.877 AC XY: 65268 AN XY: 74422

African (AFR) AF: 0.950 AC: 39490 AN: 41560

American (AMR) AF: 0.855 AC: 13066 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.895 AC: 3105 AN: 3468

East Asian (EAS) AF: 0.682 AC: 3529 AN: 5174

South Asian (SAS) AF: 0.842 AC: 4060 AN: 4820

European-Finnish (FIN) AF: 0.843 AC: 8940 AN: 10602

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.866 AC: 58892 AN: 68006

Other (OTH) AF: 0.877 AC: 1849 AN: 2108

Alfa AF: 0.873 Hom.: 81764

Bravo AF: 0.884

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.51
DANN	Benign	0.76
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs833052; hg19: chr6-43723335;