rs1377689

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_037884.1(LOC100507053):​n.428+11352A>G variant causes a intron, non coding transcript 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: LOC100507053 NR_037884.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.278

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC100507053	NR_037884.1	n.428+11352A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000500358.6	n.428+11352A>G		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.876

Gnomad4 AMR AF: 0.798

Gnomad4 ASJ AF: 0.698

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.884

Gnomad4 FIN AF: 0.774

Gnomad4 NFE AF: 0.720

Gnomad4 OTH AF: 0.762

Alfa AF: 0.755 Hom.: 5454

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1377689; hg19: chr4-100021787;