rs1928313

Positions:

• chr1-104111459-C-T

Variant summary

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

The ENST00000634888.1(ENSG00000293061):​n.735+37555C>T 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 0.0434 in 152,210 control chromosomes in the GnomAD database, including 303 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 0.043 (303 hom., cov: 32)
• Consequence: ENST00000634888.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.409

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000634888.1	n.735+37555C>T		intron_variant, non_coding_transcript_variant		5
	ENST00000634580.1	n.923-14103C>T		intron_variant, non_coding_transcript_variant		5
	ENST00000634997.1	n.252-14103C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0432 AC: 6577 AN: 152092 Hom.: 301 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0252

Gnomad ASJ AF: 0.0268

Gnomad EAS AF: 0.0168

Gnomad SAS AF: 0.0339

Gnomad FIN AF: 0.00933

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0134

Gnomad OTH AF: 0.0407

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

GnomAD4 genome AF: 0.0434 AC: 6605 AN: 152210 Hom.: 303 Cov.: 32 AF XY: 0.0439 AC XY: 3268 AN XY: 74422

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.0251

Gnomad4 ASJ AF: 0.0268

Gnomad4 EAS AF: 0.0168

Gnomad4 SAS AF: 0.0344

Gnomad4 FIN AF: 0.00933

Gnomad4 NFE AF: 0.0134

Gnomad4 OTH AF: 0.0402

Alfa AF: 0.0289 Hom.: 32

Bravo AF: 0.0481

Asia WGS AF: 0.0330 AC: 114 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	0.77
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1928313; hg19: chr1-104654081;