1-19331678-C-T

Position:

• chr1-19331678-C-T

Variant summary

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

The XM_047423394.1(SLC66A1):​c.*111C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 152,142 control chromosomes in the GnomAD database, including 3,044 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 0.19 (3044 hom., cov: 33)
• Consequence: SLC66A1 XM_047423394.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.656

Genes affected

SLC66A1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC66A1	XM_047423394.1	c.*111C>T		3_prime_UTR_variant	2/2
SLC66A1	NR_109848.2	n.1889C>T		non_coding_transcript_exon_variant	10/10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28532 AN: 152022 Hom.: 3047 Cov.: 33

Gnomad AFR AF: 0.0843

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.188 AC: 28532 AN: 152142 Hom.: 3044 Cov.: 33 AF XY: 0.192 AC XY: 14307 AN XY: 74356

Gnomad4 AFR AF: 0.0843

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.207

Gnomad4 EAS AF: 0.204

Gnomad4 SAS AF: 0.211

Gnomad4 FIN AF: 0.292

Gnomad4 NFE AF: 0.223

Gnomad4 OTH AF: 0.181

Alfa AF: 0.207 Hom.: 473

Bravo AF: 0.179

Asia WGS AF: 0.190 AC: 657 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.8
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12117357; hg19: chr1-19658172; COSMIC: COSV64320747;