chr6-4677726-T-C

Variant names:

• chr6-4677726-T-C
• rs2073042
• ENST00000716074.1:n.721+72A>G

Variant summary

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

The ENST00000716074.1(ENSG00000284823):​n.721+72A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 152,014 control chromosomes in the GnomAD database, including 4,321 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 0.22 (4321 hom., cov: 33)
• Consequence: ENSG00000284823 ENST00000716074.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.123
• Publications: 4 publications found

Genes affected

ENSG00000284823 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000284823	ENST00000716074.1	n.721+72A>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32802 AN: 151896 Hom.: 4321 Cov.: 33

Gnomad AFR AF: 0.0746

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.179

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.216 AC: 32811 AN: 152014 Hom.: 4321 Cov.: 33 AF XY: 0.221 AC XY: 16444 AN XY: 74286

African (AFR) AF: 0.0748 AC: 3100 AN: 41470

American (AMR) AF: 0.220 AC: 3353 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 690 AN: 3472

East Asian (EAS) AF: 0.322 AC: 1663 AN: 5158

South Asian (SAS) AF: 0.356 AC: 1714 AN: 4818

European-Finnish (FIN) AF: 0.310 AC: 3272 AN: 10554

Middle Eastern (MID) AF: 0.166 AC: 48 AN: 290

European-Non Finnish (NFE) AF: 0.267 AC: 18125 AN: 67964

Other (OTH) AF: 0.202 AC: 426 AN: 2104

Alfa AF: 0.228 Hom.: 761

Bravo AF: 0.200

Asia WGS AF: 0.320 AC: 1112 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.9
DANN	Benign	0.63
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs2073042; hg19: chr6-4677960;