chr22-38080269-C-T

Position:

• chr22-38080269-C-T

Variant summary

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

The NM_013356.3(SLC16A8):​c.1198+571G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 152,032 control chromosomes in the GnomAD database, including 4,698 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).

• Frequency: Genomes: 𝑓 0.24 (4698 hom., cov: 32)
• Consequence: SLC16A8 NM_013356.3 intron
• Clinical Significance: not provided no classification provided O:1
• Conservation: PhyloP100: 0.689

Genes affected

SLC16A8 (HGNC:16270): (solute carrier family 16 member 8) SLC16A8 is a member of a family of proton-coupled monocarboxylate transporters that mediate lactate transport across cell membranes (Yoon et al., 1999 [PubMed 10493836]).[supplied by OMIM, Apr 2010]

LOC105373027 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC16A8	NM_013356.3	c.1198+571G>A		intron_variant		ENST00000681075.2	NP_037488.2
LOC105373027	XR_938249.3	n.844C>T		non_coding_transcript_exon_variant	3/3
SLC16A8	NM_001394131.1	c.-80-1565G>A		intron_variant			NP_001381060.1
SLC16A8	XM_017028685.2	c.1198+571G>A		intron_variant			XP_016884174.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC16A8	ENST00000681075.2	c.1198+571G>A		intron_variant			NM_013356.3	ENSP00000506669	P1
SLC16A8	ENST00000320521.10	c.1198+571G>A		intron_variant		1		ENSP00000321735	P1
SLC16A8	ENST00000469516.5	n.107-1565G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36517 AN: 151914 Hom.: 4700 Cov.: 32

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.226

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.240 AC: 36547 AN: 152032 Hom.: 4698 Cov.: 32 AF XY: 0.240 AC XY: 17816 AN XY: 74330

Gnomad4 AFR AF: 0.330

Gnomad4 AMR AF: 0.258

Gnomad4 ASJ AF: 0.215

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.197

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.198

Gnomad4 OTH AF: 0.249

Alfa AF: 0.208 Hom.: 5006

Bravo AF: 0.251

Asia WGS AF: 0.186 AC: 647 AN: 3478

ClinVar

Significance: not provided

Submissions summary: Other:1

Revision: no classification provided

Submissions by phenotype

not provided Other:1

not provided, no classification provided

not provided

Department of Ophthalmology and Visual Sciences Kyoto University

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	13
DANN	Benign	0.68

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.15		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs8135665; hg19: chr22-38476276;