rs6995588

Variant names:

• chr8-60091338-C-T
• rs6995588
• ENST00000655001.1:n.387-3672C>T

Variant summary

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

The ENST00000655001.1(ENSG00000254775):​n.387-3672C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0948 in 151,810 control chromosomes in the GnomAD database, including 2,057 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 0.095 (2057 hom., cov: 32)
• Consequence: ENSG00000254775 ENST00000655001.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00800
• Publications: 11 publications found

Genes affected

ENSG00000254775 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375861	XR_001745714.3	n.632+16615C>T		intron_variant	Intron 4 of 4
LOC105375861	XR_007060918.1	n.354+16615C>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000254775	ENST00000655001.1	n.387-3672C>T		intron_variant	Intron 3 of 3
ENSG00000254775	ENST00000655977.1	n.360+16615C>T		intron_variant	Intron 3 of 3
ENSG00000254775	ENST00000658208.1	n.355-14668C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0947 AC: 14363 AN: 151692 Hom.: 2054 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0507

Gnomad ASJ AF: 0.0121

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.0326

Gnomad FIN AF: 0.00463

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.00319

Gnomad OTH AF: 0.0737

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

GnomAD4 genome AF: 0.0948 AC: 14384 AN: 151810 Hom.: 2057 Cov.: 32 AF XY: 0.0937 AC XY: 6955 AN XY: 74196

African (AFR) AF: 0.297 AC: 12260 AN: 41226

American (AMR) AF: 0.0506 AC: 772 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0121 AC: 42 AN: 3468

East Asian (EAS) AF: 0.139 AC: 717 AN: 5168

South Asian (SAS) AF: 0.0324 AC: 156 AN: 4816

European-Finnish (FIN) AF: 0.00463 AC: 49 AN: 10578

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.00319 AC: 217 AN: 67970

Other (OTH) AF: 0.0734 AC: 155 AN: 2112

Alfa AF: 0.0387 Hom.: 1706

Bravo AF: 0.107

Asia WGS AF: 0.0880 AC: 304 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.9
DANN	Benign	0.71
PhyloP100		-0.0080

Splicing

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

Other links and lift over

dbSNP: rs6995588; hg19: chr8-61003897;