ENST00000586142.5:c.-106A>G

Variant names:

• chr18-45730215-A-G
• rs12605147
• ENST00000586142.5:c.-106A>G

Variant summary

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

The ENST00000586142.5(SLC14A1):​c.-106A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 1,396,834 control chromosomes in the GnomAD database, including 11,346 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 0.14 (1969 hom., cov: 33)
  • Exomes 𝑓: 0.096 (9377 hom.)
• Consequence: SLC14A1 ENST00000586142.5 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.306
• Publications: 8 publications found

Genes affected

SLC14A1 (HGNC:10918): (solute carrier family 14 member 1 (Kidd blood group)) The protein encoded by this gene is a membrane transporter that mediates urea transport in erythrocytes. This gene forms the basis for the Kidd blood group system. [provided by RefSeq, Mar 2009]

ENSG00000288545 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC14A1	NM_015865.7	c.-21-85A>G		intron_variant	Intron 2 of 9	ENST00000321925.9	NP_056949.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC14A1	ENST00000321925.9	c.-21-85A>G		intron_variant	Intron 2 of 9	1	NM_015865.7	ENSP00000318546.4

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20932 AN: 152058 Hom.: 1966 Cov.: 33

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.0769

Gnomad NFE AF: 0.0679

Gnomad OTH AF: 0.113

GnomAD4 exome AF: 0.0960 AC: 119518 AN: 1244658 Hom.: 9377 Cov.: 17 AF XY: 0.0994 AC XY: 61112 AN XY: 614522

African (AFR) AF: 0.199 AC: 5563 AN: 27982

American (AMR) AF: 0.208 AC: 5924 AN: 28450

Ashkenazi Jewish (ASJ) AF: 0.0976 AC: 1916 AN: 19636

East Asian (EAS) AF: 0.390 AC: 14711 AN: 37710

South Asian (SAS) AF: 0.250 AC: 16439 AN: 65632

European-Finnish (FIN) AF: 0.115 AC: 5586 AN: 48426

Middle Eastern (MID) AF: 0.103 AC: 363 AN: 3522

European-Non Finnish (NFE) AF: 0.0655 AC: 63005 AN: 961254

Other (OTH) AF: 0.115 AC: 6011 AN: 52046

GnomAD4 genome AF: 0.138 AC: 20960 AN: 152176 Hom.: 1969 Cov.: 33 AF XY: 0.145 AC XY: 10791 AN XY: 74414

African (AFR) AF: 0.197 AC: 8197 AN: 41518

American (AMR) AF: 0.184 AC: 2810 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.100 AC: 348 AN: 3468

East Asian (EAS) AF: 0.406 AC: 2099 AN: 5166

South Asian (SAS) AF: 0.268 AC: 1290 AN: 4814

European-Finnish (FIN) AF: 0.123 AC: 1306 AN: 10592

Middle Eastern (MID) AF: 0.0828 AC: 24 AN: 290

European-Non Finnish (NFE) AF: 0.0679 AC: 4619 AN: 68014

Other (OTH) AF: 0.112 AC: 238 AN: 2116

Alfa AF: 0.140 Hom.: 705

Bravo AF: 0.143

Asia WGS AF: 0.316 AC: 1095 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	6.9
DANN	Benign	0.86
PhyloP100		0.31
PromoterAI		0.0016	Neutral
Mutation Taster		=299/1	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs12605147; hg19: chr18-43310180;