rs1998359

Variant names:

• chr14-37607943-C-G
• rs1998359
• NM_001310135.5:c.-16+1201C>G

Your query was ambiguous. Multiple possible variants found:

• chr14-37607943-C-G
• chr14-37607943-C-T

Variant summary

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

The NM_001310135.5(TTC6):​c.-16+1201C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 152,168 control chromosomes in the GnomAD database, including 3,381 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 0.20 (3381 hom., cov: 32)
• Consequence: TTC6 NM_001310135.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.76
• Publications: 15 publications found

Genes affected

TTC6 (HGNC:19739): (tetratricopeptide repeat domain 6)

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 (SAS) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001310135.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTC6	NM_001310135.5	MANE Select	c.-16+1201C>G		intron	N/A	NP_001297064.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTC6	ENST00000553443.6	TSL:5 MANE Select	c.-16+1201C>G		intron	N/A	ENSP00000451131.1

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30283 AN: 152050 Hom.: 3379 Cov.: 32

Gnomad AFR AF: 0.0956

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.199 AC: 30290 AN: 152168 Hom.: 3381 Cov.: 32 AF XY: 0.203 AC XY: 15092 AN XY: 74390

African (AFR) AF: 0.0955 AC: 3967 AN: 41536

American (AMR) AF: 0.199 AC: 3037 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 919 AN: 3466

East Asian (EAS) AF: 0.114 AC: 591 AN: 5178

South Asian (SAS) AF: 0.265 AC: 1275 AN: 4818

European-Finnish (FIN) AF: 0.283 AC: 2989 AN: 10562

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.247 AC: 16801 AN: 68000

Other (OTH) AF: 0.220 AC: 465 AN: 2112

Alfa AF: 0.123 Hom.: 220

Bravo AF: 0.186

Asia WGS AF: 0.169 AC: 590 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.096
DANN	Benign	0.71
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs1998359; hg19: chr14-38077148;