rs16865440

Variant names:

• chr2-177608681-C-T
• rs16865440
• ENST00000357045.4:n.85+5508C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000357045.4(ENSG00000237655):​n.85+5508C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0113 in 152,196 control chromosomes in the GnomAD database, including 26 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 0.011 (26 hom., cov: 32)
• Consequence: ENSG00000237655 ENST00000357045.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.239
• Publications: 1 publications found

Genes affected

ENSG00000237655 (HGNC:58181):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BS1: Variant frequency is greater than expected in population eas. GnomAd4 allele frequency = 0.0113 (1724/152196) while in subpopulation EAS AF = 0.0289 (150/5182). AF 95% confidence interval is 0.0252. There are 26 homozygotes in GnomAd4. There are 870 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 26 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IFT70A-AS1	NR_198966.1	n.114+5508C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000237655	ENST00000357045.4	n.85+5508C>T		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.0113 AC: 1719 AN: 152078 Hom.: 25 Cov.: 32

Gnomad AFR AF: 0.0248

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00982

Gnomad ASJ AF: 0.00173

Gnomad EAS AF: 0.0289

Gnomad SAS AF: 0.000829

Gnomad FIN AF: 0.00255

Gnomad MID AF: 0.0159

Gnomad NFE AF: 0.00478

Gnomad OTH AF: 0.0124

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

GnomAD4 genome AF: 0.0113 AC: 1724 AN: 152196 Hom.: 26 Cov.: 32 AF XY: 0.0117 AC XY: 870 AN XY: 74412

African (AFR) AF: 0.0248 AC: 1031 AN: 41528

American (AMR) AF: 0.00981 AC: 150 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.00173 AC: 6 AN: 3472

East Asian (EAS) AF: 0.0289 AC: 150 AN: 5182

South Asian (SAS) AF: 0.000830 AC: 4 AN: 4820

European-Finnish (FIN) AF: 0.00255 AC: 27 AN: 10594

Middle Eastern (MID) AF: 0.0137 AC: 4 AN: 292

European-Non Finnish (NFE) AF: 0.00478 AC: 325 AN: 67994

Other (OTH) AF: 0.0128 AC: 27 AN: 2112

Alfa AF: 0.00873 Hom.: 2

Bravo AF: 0.0129

Asia WGS AF: 0.0170 AC: 59 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	5.5
DANN	Benign	0.70
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs16865440; hg19: chr2-178473409;