rs71607999

Variant names:

• chr4-188269957-G-A
• rs71607999
• ENST00000777700.1:n.237-5734G>A

Variant summary

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

The ENST00000777700.1(ENSG00000301287):​n.237-5734G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 151,738 control chromosomes in the GnomAD database, including 1,342 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 0.12 (1342 hom., cov: 31)
• Consequence: ENSG00000301287 ENST00000777700.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 4 publications found

Genes affected

ENSG00000301287 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301287	ENST00000777700.1	n.237-5734G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17496 AN: 151618 Hom.: 1343 Cov.: 31

Gnomad AFR AF: 0.0303

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.00777

Gnomad SAS AF: 0.0989

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.115 AC: 17498 AN: 151738 Hom.: 1342 Cov.: 31 AF XY: 0.114 AC XY: 8456 AN XY: 74128

African (AFR) AF: 0.0302 AC: 1250 AN: 41408

American (AMR) AF: 0.130 AC: 1976 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 897 AN: 3470

East Asian (EAS) AF: 0.00779 AC: 40 AN: 5136

South Asian (SAS) AF: 0.100 AC: 482 AN: 4818

European-Finnish (FIN) AF: 0.133 AC: 1393 AN: 10488

Middle Eastern (MID) AF: 0.234 AC: 68 AN: 290

European-Non Finnish (NFE) AF: 0.162 AC: 10979 AN: 67886

Other (OTH) AF: 0.129 AC: 270 AN: 2098

Alfa AF: 0.134 Hom.: 203

Asia WGS AF: 0.0620 AC: 215 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.29
DANN	Benign	0.76
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs71607999; hg19: chr4-189191111;