rs4988822

Variant names:

• chr6-32431198-C-T
• rs4988822
• ENST00000766007.1:n.280-467G>A

Variant summary

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

The ENST00000766007.1(ENSG00000299747):​n.280-467G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 150,502 control chromosomes in the GnomAD database, including 4,937 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 0.23 (4937 hom., cov: 31)
• Consequence: ENSG00000299747 ENST00000766007.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.194
• Publications: 11 publications found

Genes affected

ENSG00000299747 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000766007.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299747	ENST00000766007.1		n.280-467G>A		intron	N/A
	ENSG00000299769	ENST00000766247.1		n.283-2894C>T		intron	N/A
	ENSG00000299769	ENST00000766248.1		n.*190C>T		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35264 AN: 150386 Hom.: 4935 Cov.: 31

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.100

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.234 AC: 35286 AN: 150502 Hom.: 4937 Cov.: 31 AF XY: 0.237 AC XY: 17402 AN XY: 73502

African (AFR) AF: 0.143 AC: 5906 AN: 41160

American (AMR) AF: 0.206 AC: 3117 AN: 15098

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 500 AN: 3448

East Asian (EAS) AF: 0.158 AC: 813 AN: 5148

South Asian (SAS) AF: 0.171 AC: 817 AN: 4768

European-Finnish (FIN) AF: 0.409 AC: 4248 AN: 10374

Middle Eastern (MID) AF: 0.0972 AC: 28 AN: 288

European-Non Finnish (NFE) AF: 0.284 AC: 19086 AN: 67224

Other (OTH) AF: 0.229 AC: 480 AN: 2094

Alfa AF: 0.241 Hom.: 2145

Bravo AF: 0.220

Asia WGS AF: 0.203 AC: 710 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.5
DANN	Benign	0.46
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs4988822; hg19: chr6-32398975;