ENST00000448991.7:n.85+1208C>G

Variant names:

• chr6-52971899-G-C
• rs17608261
• ENST00000448991.7:n.85+1208C>G

Variant summary

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

The ENST00000448991.7(ENSG00000291036):​n.85+1208C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0298 in 152,298 control chromosomes in the GnomAD database, including 109 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 0.030 (109 hom., cov: 32)
• Consequence: ENSG00000291036 ENST00000448991.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.216
• Publications: 2 publications found

Genes affected

ENSG00000291036 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0298 (4533/152298) while in subpopulation NFE AF = 0.0473 (3216/68024). AF 95% confidence interval is 0.0459. There are 109 homozygotes in GnomAd4. There are 2070 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 109 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000448991.7. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000291036	ENST00000448991.7	TSL:3	n.85+1208C>G		intron	N/A
	ENSG00000291036	ENST00000763228.1		n.48+1208C>G		intron	N/A
	ENSG00000291036	ENST00000763229.1		n.29+1208C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0298 AC: 4539 AN: 152180 Hom.: 110 Cov.: 32

Gnomad AFR AF: 0.00871

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0354

Gnomad ASJ AF: 0.0432

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00539

Gnomad FIN AF: 0.00565

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0473

Gnomad OTH AF: 0.0411

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

GnomAD4 genome AF: 0.0298 AC: 4533 AN: 152298 Hom.: 109 Cov.: 32 AF XY: 0.0278 AC XY: 2070 AN XY: 74470

African (AFR) AF: 0.00869 AC: 361 AN: 41556

American (AMR) AF: 0.0353 AC: 540 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0432 AC: 150 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5180

South Asian (SAS) AF: 0.00539 AC: 26 AN: 4824

European-Finnish (FIN) AF: 0.00565 AC: 60 AN: 10626

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.0473 AC: 3216 AN: 68024

Other (OTH) AF: 0.0402 AC: 85 AN: 2112

Alfa AF: 0.0160 Hom.: 7

Bravo AF: 0.0316

Asia WGS AF: 0.00635 AC: 22 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.71
DANN	Benign	0.66
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs17608261; hg19: chr6-52836697;