rs10953356

Variant names:

• chr7-77820281-A-G
• rs10953356
• NM_001395272.1:c.-35-19940A>G

Your query was ambiguous. Multiple possible variants found:

• chr7-77820281-A-G
• chr7-77820281-A-T

Variant summary

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

The NM_001395272.1(PHTF2):​c.-35-19940A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 152,088 control chromosomes in the GnomAD database, including 4,364 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 (4364 hom., cov: 32)
• Consequence: PHTF2 NM_001395272.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131
• Publications: 4 publications found

Genes affected

PHTF2 (HGNC:13411): (putative homeodomain transcription factor 2) Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

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 (SAS) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PHTF2	NM_001395272.1	c.-35-19940A>G		intron_variant	Intron 1 of 18	ENST00000422959.8	NP_001382201.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PHTF2	ENST00000422959.8	c.-35-19940A>G		intron_variant	Intron 1 of 18	5	NM_001395272.1	ENSP00000403042.2

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34952 AN: 151970 Hom.: 4361 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.230 AC: 34965 AN: 152088 Hom.: 4364 Cov.: 32 AF XY: 0.228 AC XY: 16960 AN XY: 74336

African (AFR) AF: 0.153 AC: 6328 AN: 41494

American (AMR) AF: 0.237 AC: 3617 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 877 AN: 3470

East Asian (EAS) AF: 0.143 AC: 741 AN: 5172

South Asian (SAS) AF: 0.294 AC: 1418 AN: 4822

European-Finnish (FIN) AF: 0.241 AC: 2553 AN: 10588

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.275 AC: 18710 AN: 67950

Other (OTH) AF: 0.238 AC: 504 AN: 2114

Alfa AF: 0.248 Hom.: 6603

Bravo AF: 0.223

Asia WGS AF: 0.220 AC: 768 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.7
DANN	Benign	0.61
PhyloP100		0.13
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs10953356; hg19: chr7-77449598;