rs7722165

Variant names:

• chr5-173507967-C-A
• rs7722165
• ENST00000827042.1:n.446+1595C>A

Variant summary

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

The ENST00000827042.1(ENSG00000253968):​n.446+1595C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.366 in 152,010 control chromosomes in the GnomAD database, including 10,395 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 0.37 (10395 hom., cov: 32)
• Consequence: ENSG00000253968 ENST00000827042.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.401
• Publications: 2 publications found

Genes affected

ENSG00000253968 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000827042.1. 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
	ENSG00000253968	ENST00000827042.1		n.446+1595C>A		intron	N/A
	ENSG00000253968	ENST00000827044.1		n.374+1595C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.366 AC: 55521 AN: 151892 Hom.: 10372 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.366 AC: 55591 AN: 152010 Hom.: 10395 Cov.: 32 AF XY: 0.369 AC XY: 27422 AN XY: 74302

African (AFR) AF: 0.293 AC: 12166 AN: 41462

American (AMR) AF: 0.463 AC: 7065 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1142 AN: 3470

East Asian (EAS) AF: 0.271 AC: 1404 AN: 5172

South Asian (SAS) AF: 0.404 AC: 1946 AN: 4822

European-Finnish (FIN) AF: 0.388 AC: 4094 AN: 10544

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.389 AC: 26459 AN: 67958

Other (OTH) AF: 0.393 AC: 830 AN: 2114

Alfa AF: 0.389 Hom.: 5628

Bravo AF: 0.367

Asia WGS AF: 0.347 AC: 1208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.3
DANN	Benign	0.86
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs7722165; hg19: chr5-172934970; COSMIC: COSV60232125;