rs1377689

Variant names:

• chr4-99100636-A-G
• rs1377689
• ENST00000500358.6:n.428+11352A>G

Your query was ambiguous. Multiple possible variants found:

• chr4-99100636-A-G
• chr4-99100636-A-T

Variant summary

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

The ENST00000500358.6(ENSG00000246090):​n.428+11352A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.789 in 152,196 control chromosomes in the GnomAD database, including 47,903 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 0.79 (47903 hom., cov: 32)
• Consequence: ENSG00000246090 ENST00000500358.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.278
• Publications: 1 publications found

Genes affected

ENSG00000246090 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100507053	NR_037884.1	n.428+11352A>G		intron_variant	Intron 1 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000246090	ENST00000500358.6	n.428+11352A>G		intron_variant	Intron 1 of 9	1
ENSG00000246090	ENST00000499178.3	n.416-1727A>G		intron_variant	Intron 1 of 2	3
ENSG00000246090	ENST00000661393.1	n.425+11352A>G		intron_variant	Intron 1 of 9

Frequencies

GnomAD3 genomes AF: 0.788 AC: 119906 AN: 152078 Hom.: 47851 Cov.: 32

Gnomad AFR AF: 0.876

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.798

Gnomad ASJ AF: 0.698

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.884

Gnomad FIN AF: 0.774

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.759

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

GnomAD4 genome AF: 0.789 AC: 120019 AN: 152196 Hom.: 47903 Cov.: 32 AF XY: 0.796 AC XY: 59262 AN XY: 74422

African (AFR) AF: 0.876 AC: 36377 AN: 41546

American (AMR) AF: 0.798 AC: 12190 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.698 AC: 2423 AN: 3472

East Asian (EAS) AF: 0.998 AC: 5183 AN: 5192

South Asian (SAS) AF: 0.884 AC: 4267 AN: 4826

European-Finnish (FIN) AF: 0.774 AC: 8185 AN: 10580

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.720 AC: 48947 AN: 67986

Other (OTH) AF: 0.762 AC: 1610 AN: 2114

Alfa AF: 0.760 Hom.: 5756

Bravo AF: 0.794

Asia WGS AF: 0.931 AC: 3235 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.65
DANN	Benign	0.66
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs1377689; hg19: chr4-100021787;