17-74255101-G-A

Variant names:

• chr17-74255101-G-A
• rs8078051
• NM_032646.6:c.1524+1268G>A

Variant summary

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

The NM_032646.6(TTYH2):​c.1524+1268G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0421 in 152,310 control chromosomes in the GnomAD database, including 416 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 0.042 (416 hom., cov: 33)
• Consequence: TTYH2 NM_032646.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.314
• Publications: 7 publications found

Genes affected

TTYH2 (HGNC:13877): (tweety family member 2) This gene encodes a member of the tweety family of proteins. Members of this family function as chloride anion channels. The encoded protein functions as a calcium(2+)-activated large conductance chloride(-) channel, and may play a role in kidney tumorigenesis. Two transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.142 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032646.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTYH2	NM_032646.6	MANE Select	c.1524+1268G>A		intron	N/A	NP_116035.5
	TTYH2	NM_001330453.2		c.1461+1268G>A		intron	N/A	NP_001317382.1	B4DKD1
	TTYH2	NM_052869.1		c.561+1268G>A		intron	N/A	NP_443101.1	Q9BSA4-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTYH2	ENST00000269346.9	TSL:1 MANE Select	c.1524+1268G>A		intron	N/A	ENSP00000269346.4	Q9BSA4-1
	TTYH2	ENST00000441391.6	TSL:1	c.561+1268G>A		intron	N/A	ENSP00000394576.2	Q9BSA4-2
	TTYH2	ENST00000876771.1		c.1518+1268G>A		intron	N/A	ENSP00000546830.1

Frequencies

GnomAD3 genomes AF: 0.0419 AC: 6382 AN: 152192 Hom.: 409 Cov.: 33

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0173

Gnomad ASJ AF: 0.00260

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000621

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.000794

Gnomad OTH AF: 0.0306

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

GnomAD4 genome AF: 0.0421 AC: 6419 AN: 152310 Hom.: 416 Cov.: 33 AF XY: 0.0405 AC XY: 3013 AN XY: 74460

African (AFR) AF: 0.145 AC: 6023 AN: 41558

American (AMR) AF: 0.0173 AC: 264 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.00260 AC: 9 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5180

South Asian (SAS) AF: 0.000414 AC: 2 AN: 4830

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10626

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.000794 AC: 54 AN: 68030

Other (OTH) AF: 0.0303 AC: 64 AN: 2112

Alfa AF: 0.0146 Hom.: 16

Bravo AF: 0.0479

Asia WGS AF: 0.00837 AC: 29 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.63
PhyloP100		-0.31
Mutation Taster		=100/0	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: rs8078051; hg19: chr17-72251240;