rs1386948

chr3-3617921-A-Cchr3-3617921-A-Gchr3-3617921-A-T

Variant summary

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

The ENST00000420000.6(ENSG00000223727):n.200+8823T>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 0.751 in 152,142 control chromosomes in the GnomAD database, including 43,197 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 0.75 (43197 hom., cov: 34)
• Consequence: ENST00000420000.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.01

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000420000.6	n.200+8823T>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.752 AC: 114261 AN: 152024 Hom.: 43172 Cov.: 34

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.834

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.743

Gnomad EAS AF: 0.570

Gnomad SAS AF: 0.736

Gnomad FIN AF: 0.780

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.801

Gnomad OTH AF: 0.756

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

GnomAD4 genome AF: 0.751 AC: 114333 AN: 152142 Hom.: 43197 Cov.: 34 AF XY: 0.749 AC XY: 55727 AN XY: 74386

Gnomad4 AFR AF: 0.699

Gnomad4 AMR AF: 0.716

Gnomad4 ASJ AF: 0.743

Gnomad4 EAS AF: 0.570

Gnomad4 SAS AF: 0.735

Gnomad4 FIN AF: 0.780

Gnomad4 NFE AF: 0.801

Gnomad4 OTH AF: 0.755

Alfa AF: 0.787 Hom.: 69050

Bravo AF: 0.744

Asia WGS AF: 0.679 AC: 2361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.27
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1386948; hg19: chr3-3659605;