rs1199393

Variant names:

• chr6-8397767-C-G
• rs1199393
• ENST00000644718.1:n.561-40196C>G

Variant summary

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

The ENST00000644718.1(ENSG00000285216):​n.561-40196C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.381 in 152,016 control chromosomes in the GnomAD database, including 14,125 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 0.38 (14125 hom., cov: 32)
• Consequence: ENSG00000285216 ENST00000644718.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.416
• Publications: 0 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.696 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.561-40196C>G		intron_variant	Intron 5 of 8
ENSG00000285216	ENST00000790387.1	n.283-40196C>G		intron_variant	Intron 3 of 5
ENSG00000285216	ENST00000790388.1	n.294-40196C>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.381 AC: 57892 AN: 151896 Hom.: 14091 Cov.: 32

Gnomad AFR AF: 0.703

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.381 AC: 57989 AN: 152016 Hom.: 14125 Cov.: 32 AF XY: 0.377 AC XY: 28008 AN XY: 74288

African (AFR) AF: 0.703 AC: 29143 AN: 41476

American (AMR) AF: 0.304 AC: 4637 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 817 AN: 3472

East Asian (EAS) AF: 0.194 AC: 1006 AN: 5174

South Asian (SAS) AF: 0.346 AC: 1668 AN: 4820

European-Finnish (FIN) AF: 0.273 AC: 2885 AN: 10550

Middle Eastern (MID) AF: 0.271 AC: 79 AN: 292

European-Non Finnish (NFE) AF: 0.250 AC: 16991 AN: 67946

Other (OTH) AF: 0.338 AC: 715 AN: 2114

Alfa AF: 0.113 Hom.: 193

Bravo AF: 0.399

Asia WGS AF: 0.342 AC: 1189 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.82
DANN	Benign	0.58
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs1199393; hg19: chr6-8398000;