ENST00000644718.1:n.560+41113A>G

Variant names:

• chr6-8348673-A-G
• rs7771933
• ENST00000644718.1:n.560+41113A>G

Variant summary

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

The ENST00000644718.1(ENSG00000285216):​n.560+41113A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 151,932 control chromosomes in the GnomAD database, including 9,986 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 0.35 (9986 hom., cov: 31)
• Consequence: ENSG00000285216 ENST00000644718.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.510
• Publications: 2 publications found

Genes affected

ENSG00000285216 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.497 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
ENSG00000285216	ENST00000644718.1	n.560+41113A>G		intron_variant	Intron 5 of 8
ENSG00000234763	ENST00000651914.1	n.312-6025T>C		intron_variant	Intron 4 of 4
ENSG00000234763	ENST00000655767.2	n.375-6025T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.345 AC: 52446 AN: 151816 Hom.: 9971 Cov.: 31

Gnomad AFR AF: 0.503

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.394

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.346 AC: 52496 AN: 151932 Hom.: 9986 Cov.: 31 AF XY: 0.337 AC XY: 25037 AN XY: 74268

African (AFR) AF: 0.503 AC: 20815 AN: 41406

American (AMR) AF: 0.274 AC: 4181 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1260 AN: 3472

East Asian (EAS) AF: 0.155 AC: 801 AN: 5164

South Asian (SAS) AF: 0.336 AC: 1612 AN: 4802

European-Finnish (FIN) AF: 0.204 AC: 2161 AN: 10570

Middle Eastern (MID) AF: 0.393 AC: 114 AN: 290

European-Non Finnish (NFE) AF: 0.302 AC: 20492 AN: 67958

Other (OTH) AF: 0.373 AC: 788 AN: 2110

Alfa AF: 0.313 Hom.: 1389

Bravo AF: 0.358

Asia WGS AF: 0.254 AC: 881 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.7
DANN	Benign	0.54
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs7771933; hg19: chr6-8348906;